This was agreed in a resolution approved by the constitutional affairs committee on Tuesday.
The move follows rising concern about the recent activities of some Brussels-based lobbyists who are looking to influence legislation.
The text, 'Transparency, accountability and integrity in the EU institutions', drafted by German Greens/EFA group deputy Sven Giegold, states that what it calls "non-transparent interest representation" may pose a "significant threat" to the integrity of policymakers.
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It suggests that all lobbyists looking to influence the legislative process should be required to sign the transparency register before being allowed to meet MEPs on Parliament's premises.
At present, lobbyists are not required to sign the register.
Commenting on the decision, Giegold said, "Today's vote calls for major steps towards greater transparency and integrity in the EU institutions, something that would help improve the public's regard for EU institutions.
"Such measures were completely lacking in Juncker's White Paper, so it has fallen to Parliament to deliver. After the scandals surrounding José Manuel Barroso and Neelie Kroes, there must be a genuine reform of the code of conduct for Commissioners.
"Former Commissioners should take a break of at least three years before they can become lobbyists, and there must be independent and rigorous examination of their new jobs at the end of their mandate.
"Under the proposals approved today, all payments to lobby organisations above €3000 must be transparent. Citizens have a right to know who is paying who in the murky world of Brussels lobbying."
"However," he added, "MEPs need to be more ambitious in keeping their own house clean. While MEPs called on the Commission to ensure that all policymakers have to disclose their meetings with lobbyists, they don't want to apply this rule to themselves."
The MEP said, "Until Parliament is prepared to make the same demands on itself as it asks of the Commission, it will not be taken seriously in negotiations."
The report was due to be voted on last September but the EPP, S&D and Liberal groups were accused of blocking it. Many of the particularly controversial rules for MEPs were subsequently decided in the Corbett report on the European Parliament's rules of procedure.
The final plenary vote is expected in the weeks to come.
The text, adopted on Tuesday by 20 votes to two against, comes after Parliament's bureau called for a "template for a voluntary legislative footprint" for MEPs.
This would allow members to set out which representatives and organisations they have consulted.
MEPs, in the resolution, also reiterate the need to withdraw access privileges from those organisations that refuse to cooperate with Parliament.
They stress that organisations that have signed the transparency register should be prohibited from employing individuals who disguise the interest parties they serve.
The resolution goes on to say that committee chairs and other lead MEPs should meet only interest groups that are registered and publish these meetings online.
This, it states, is because such members have a special responsibility to be transparent in their contacts with lobbyists inside and outside Parliament.
The resolution also highlights the need to strengthen restrictions on former European Commissioners taking part in lobbying activities, by extending their cooling-off period to three years after they leave office.
It also states that decisions on former Commissioners' new role must be taken by an authority as "independent as possible of those affected by its decisions."
This follows the ongoing row over the so called revolving door practice that has seen a series of ex-Commissioners take up well-paid roles in the private sector soon after leaving office.
New rules to improve transparency and efficiency were included in Parliament's new rules of procedure, approved in December. These require that MEPs' declarations of financial interests be more detailed, regularly updated and checked.
Former MEPs will, according to the new rules, have to inform Parliament when they take a new job as a lobbyist. The code of conduct for MEPs was also revised, to include an explicit ban on serving MEPs taking paid lobbying jobs.