Labour MPs have been told to cancel leave and be prepared for a three-line whip as the party enters another difficult week in which it will push for a series of amendments before a final vote on the Brexit bill.

A copy of the week’s whipping schedule – sent to politicians and seen by the Guardian – confirms that the party will be asking all its politicians to line up together on Wednesday.

But Jeremy Corbyn has hinted that frontbenchers who defy the official position will not face the sack, telling BBC Radio 4 that he is a “very lenient person”.

Labour’s chief whip, Nick Brown, could face anger at Monday’s meeting of the parliamentary party over the issue amid questions about the meaning of a three-line whip if rebels remain on the frontbench.

Some MPs are annoyed about last week’s vote on the bill’s second reading in which three shadow cabinet members and some ministers resigned but others, including whips, were not punished.

There is also some scepticism about the fact that the shadow home secretary, Diane Abbott, said she was unable to vote because she went home with a migraine.

The Guardian understands that she informed Corbyn’s office before leaving the House of Commons, where the rest of the party helped passed the bill despite a rebellion of 47 Labour MPs.

One person working in the whips’ office said it was difficult to be authoritative with colleagues when there was so much inconsistency as to the outcome of a decision to rebel. Another MP said: “The Labour whips’ office is turning into an advisory service.”

But others were much more sympathetic about the position Labour finds itself in, given the number of MPs representing heavy leave constituencies and those with large remain support. London MPs including Abbott, the shadow Brexit secretary, Keir Starmer, and the shadow foreign secretary, Emily Thornberry, have received thousands of emails from constituents angry about Labour’s decision to back the government over article 50.

Corbyn ordered his party to take that line at the second reading last week, but will now try to win a series of amendments that aim to force the government to regularly report on the negotiations, make the final vote on the deal more meaningful and guarantee protections for British workers.

In theory, Labour could choose to abstain on Wednesday’s final vote if all the amendments fail, but senior figures have suggested that is very unlikely, and whips say they have been told to expect the same position again.

However, sources insisted the final decision would only be made this week after Corbyn meets with his party’s Brexit sub-committee – including Abbott and Starmer – and then his full shadow cabinet on Tuesday. They said the inclusion of a three-line whip on a document to MPs was also referring to amendments.

Thornberry told the BBC’s Andrew Marr Show that it was unfair to brand the party as hopelessly divided over the issue. “The Labour party is a national party, and we represent the nation, and the nation is divided on this. It is very difficult and many MPs representing majority-remain constituencies have this very difficult balancing act: do I represent my constituency, or do I represent the nation?” Thornberry said.

She added: “Labour, as a national party, have a clear view. We have been given our instructions. We lost the referendum. We fought to stay in Europe but the public have spoken and so we do as we’re told. But the important thing now is not to give Theresa May a blank cheque, we have to make sure we get the right deal for the country.”

The bill will be debated over three days this week, with Labour’s shadow Brexit minister, Matthew Pennycook, starting for the party in the Commons on Monday, pushing for the government to give more parliamentary oversight to the Brexit process.

Labour will also press for a unilateral guarantee to EU citizens and for a meaningful final vote before the deal goes to the European parliament.