Talks paving the way for the UK to leave the EU do not start until March, when Britain triggers article 50 of the Lisbon treaty.
But MEPs, led by Parliament President Martin Schulz, have already voiced concerns that the institution - which, officially at least, must sign off the final agreement between the EU and the UK - will be marginalised during the discussions.
Schulz, due to step down as President next month, has warned that any deal reached could be vetoed if MEPs are not fully involved.
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The German deputy, in the letter to European council president Donald Tusk ahead of a Brussels summit on Thursday, warned that if the Parliament has only a "secondary role" it cannot exclude deciding to "draw up its own detailed arrangements governing its interaction" with the EU negotiator, Michel Barnier and the UK government.
At Thursday's one day summit, the leaders agreed that Barnier will lead talks for the EU and Tusk said the "short, informal meeting" had "reconfirmed our principles, meaning the indivisibility of the four freedoms, the balance of rights and obligations and the rule 'no negotiations without notification'."
A statement agreed by all member states and issued afterwards directly addressed the demand from Schulz, and others, that MEPs have a full say in the Brexit process, albeit relegating reference to this to the last paragraph of the official communique.
The key sentence reads, "The presidency of the Council will be prepared to inform and exchange views with the European Parliament before and after each meeting of the general affairs council. The President of the European Parliament will be invited to be heard at the beginning of meetings of the European Council.
"The Union negotiator will be invited to keep the European Parliament closely and regularly informed throughout the negotiation."
Earlier, EU leaders said negotiations over the UK's exit would be approached in "a spirit of trust and unity."
However, there were accusations that UK Prime Minister Theresa May had herself been sidelined during the European Council summit meeting.
This view was reinforced when she was not invited to join the 27 other EU leaders who later met for a post-summit dinner to discuss their approach to Brexit negotiations.
May held a 20-minute meeting before the start of the summit with both Barnier and Parliament's Brexit negotiator, Guy Verhofstadt.
They discussed ensuring a smooth, orderly Brexit, according to an official in May's office. Britain's approach is to engage with Parliament on Brexit, and any disagreement between Parliament and the Commission is for them to work out, the official said.
The same officials also said that Barnier is working on the basis that Britain will face a Brexit bill of as much as €60bn to cover outstanding liabilities with the EU.
May gave a short update on Brexit to her counterparts during the summit, in which she outlined two issues, the first being the UK government's appeal against a high court ruling that she must seek Parliamentary approval before triggering Brexit.
The second issue was that she wants to have the question of UK citizens living in Europe and European citizens living in the UK dealt with "in the early parts of discussions that will take place."
The summit also discussed other issues, including migration, security, economic and social development and youth, but was partly overshadowed by Brexit.
Speaking in the margins of the summit, Ray Finch, a Ukip MEP, was scathing of Verhofstadt's suggestions that Parliament might open separate negotiations with the British authorities, branding it as "just comical."
Finch told this website, "Why would the British government be interested in negotiating with someone without the real power to decide? The thought is ridiculous beyond belief.
"The British public voted to leave the single market, take back control of our laws and stop EU mass immigration as soon as possible. We would prefer to deal with the interlocutor with the real power. That is the Council, not the Parliament. Ultimately, we want to achieve our aims. How and with whom we do get there is secondary."
In his formal address to the EU leaders, Schulz said the Brexit process should not be allowed to become an "emotional affair."
He said, "Until the UK's withdrawal process has been completed we remain a Union of the 28. I have stated on several occasions that this means that the UK remains a member that enjoys all rights and benefits of EU membership, but at the same time it also fulfils its duties and allows the other members to advance their cooperation if they so desire."
Schulz, who is due to return to German domestic politics in the New Year, added, "The EU27 will continue to hold strong on the common line of no-negotiation without notification.
"This is because notification represents the first moment at which some official clarity can be provided by the British government to the whole process. Brexit is an evolving issue and it is for the UK to first outline what relationship it wants with the EU, not the other way round.
"Having said this, I think that inside the EU certain fundamental principles have already been decided upon, and the 27 should be firm on them: we have decided that the four freedoms go together and that Brexit could not be a better deal than remaining in the EU."
In his speech, his last at an EU summit, he said Parliament "has begun working closely with the Commission on the matter and we have full trust that it is best placed to act as the EU's honest broker.
"The Commission has clearly grasped the need to involve the parliament from the start, thereby increasing the chances of ownership and a successful conclusion of the withdrawal negotiation."
Schulz went on, "The three phase model that the Commission has chosen to base its work on is indeed the right one. It allows some quick clarity, through a rapid conclusion of the withdrawal agreement, while on the other hand allowing for an orderly, and gradual move towards the new relationship.
"The UK and the EU are, and will remain, closely connected and there are too many lives on the line for an erratic, quick and total separation."
He said, "Brexit has occupied the last year of my mandate quite intensively, before and after the referendum. I have never hidden that I would have preferred the UK to remain in the EU, but I urge you all to now work in a spirit of loyal cooperation along the broad guideline given by the electorate: an exit of the UK from the EU.
"We cannot allow the Brexit process to become an emotional affair, nor should we turn it into a legal maze from which exit is extremely difficult. We must not feed populists' unfounded claims that the EU is the master of all evil.
"We must also use this moment to concretely reflect on what we want the EU to be in the future and to provide it with the necessary tools."
Schulz said, "Brexit comes with dangers which we must avoid but also opportunities which we must seize."