The strike on Thursday by the Walloon wing of the rail unions continued into Friday.
Ludo Sempels, of the Socialist trades union, told VRT news, a Belgian TV network, that talks to find a way of ending the strike would begin again on Friday.
On Thursday, almost no trains were running in Wallonia and this had consequences for services in Flanders.
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Train services that start in Wallonia and pass through Flanders were particularly badly hit, while other services remain relatively unaffected.
Friday was another difficult day for tens of thousands of commuters with rail traffic in Wallonia at a standstill and many services in Flanders also hit as they also serve part of Wallonia.
SNCB are advising passengers to check its website and social media for the very latest information. But a spokesperson told this website that as the SNCB website and app are being used much more than normal those using them "are asked to be patient."
The strike this week, just the latest to hit the Belgian rail network, is the result of discontent among workers at train depots about measures that would see them lose time off given to them for working overtime and anti-social hours.
They are also unhappy about a savings plan drafted by the country's former Transport Minister Jacqueline Galant, a Francophone Liberal.
Socialist and Christian trades union are also planning to suspend rail services on 31 May. This is part of a general strike in the public sector that day.
Many public services will be halted, including the public-owned national rail company.
Another protest action is planned on 24 June when rail services are expected to be disrupted yet again.
The industrial action is part of a series of protests against the policies adopted by the conservative government of Prime Minister Charles Michel, including continuing austerity measures. It includes three major demonstrations and two days of strikes.
A students' organisation says they, among others, are incensed with the rail strikes as they come in the middle of the exam season.
Jonathan Hooft of the Flemish students' association, said, "Students will now have to find an alternative to make it to their exams. This brings extra stress and uncertainty. Some students will have to leave home much earlier."
The rail stoppages this week follow a protest in Brussels on Tuesday when some 60,000 workers marched against the government's austerity measures.
The Brussels demonstration targeted planned cuts to the welfare system, budget cuts in public service and education, and a labour reform allowing bosses to introduce a 45-hour work week and impose overtime without extra pay.
General Federation of Workers' official Michel Meyer told Le Soir newspaper, "Everybody will be hurt very much by the abandonment of the 38-hour week, the increased recourse to temporary workers, the absence of coordination and the under-financing of (public services) or pensions."
Negotiations to resolve the dispute are not due to start until Friday afternoon.
Currently, few if any trains at all are running in Wallonia while in Flanders, depending on the route, between 60 per cent and 90 per cent of services are operating.
The spokesman for the Belgian rail company NMBS Bart Schols told VRT News, "There is little or no rail service in Wallonia.Things are better in Flanders, be we are suffering the effect of rolling stock that isn’t coming from Wallonia”.
Thomas Baeken, of the rail infrastructure company Infrabel, said,that just five of Belgium’s 150 signal boxes are not manned. All the signal boxes that are strike-bound are in Wallonia.
A month after the mass anti-austerity protest in November 2014, trade unions brought Belgium to a standstill as the biggest general strike in years grounded flights, cut international rail links and shut ports.
The growing movement against austerity in Belgium coincides with an escalating wave of strikes in France.