MPs Harry Cohen and Neil Gerrard have stood firm over their opposition to university top-up fees.
They voted against the Government over the issue on Tuesday night in the House of Commons. But the Higher Education Bill was passed by just five votes.
Walthamstow MP Mr Gerrard said: "I wish it had not happened but it went through.
"I thought the Government might win, but with the smallest margin. The actual Bill still has to go through and all the detail still has to be discussed, so it is quite possible there will be arguments over that.
"The worrying issue is still over the variable fees. There is a cap on universities at charging £3,000 but the question is what will happen to that figure in the future.
"What the Government has to learn from this is not force something through that Labour members are not happy with. We now need to have a proper discussion about all this."
Leyton MP Mr Cohen was also among the 90 Labour MPs who refused to go back on their party's manifesto pledge not to introduce top-up fees.
He said: "When the cap comes off, the fees will soar, maintenance grants will not keep pace and student debt will rise hugely.
"The concessions of a maintenance grant for students from poor backgrounds and a cap on the levels of fees for a period do not mitigate my concerns.
"I feel that investment should in the main come from a higher rate income tax. Over 80 per cent of those who would pay such a tax are graduates."
Comments: Our rules
We want our comments to be a lively and valuable part of our community - a place where readers can debate and engage with the most important local issues. The ability to comment on our stories is a privilege, not a right, however, and that privilege may be withdrawn if it is abused or misused.
Please report any comments that break our rules.
Read the rules hereComments are closed on this article