Agreeing to amendable motions would allow parliament to direct government on its approach to exiting the European Union, binding the prime minister's hands and making it harder to secure a good deal for the UK.
He told Sky News the thought of that "wakes me up in the middle of the night in a cold sweat".
The government has promised lawmakers a vote on the final deal, but the issue at stake is what happens if they reject it.
"I shall lobby the prime minister and the leader of the House Andrea Leadsom for the government to give us time to get it through", he said.
However, they have fallen into a row with lawmakers from May's Conservative Party who want parliament to have a say in the exit process if talks in Brussels fail to reach an acceptable divorce deal.
"It is absolutely right Parliament can not micromanage the government's negotiating".
"Our original amendment struck the right balance between respecting the tests set out by the government as well as delivering on the aims of Dominic Grieve's own amendment".
"Whichever way the vote ultimately goes, the idea that the Government is going to be endangered by this difference of view within the House of Commons which might lead to its defeat is complete nonsense".
CSU leader to reject migrants at German border if no European Union deal
Seehofer said his party was keen to find a way to limit the number of asylum seekers arriving in Germany. The two parties govern with the center-left Social Democrats.
Last week, the prime minister avoided defeat on the issue - but the would-be rebels said they were not happy with the concessions they were subsequently offered in return for not voting against the government.
She insisted she had been listening to the concerns of critics but said the legislation must not restrict her freedom in talks with Brussels.
She said part of it would be funded by "the money we no longer spend on our annual membership subscription to the European Union", raising the ire of Remain supporters, who say the figures don't add up.
Ministers have so far agreed to give parliament a symbolic vote on the government's strategy if its initial exit deal is rejected, but not to give parliament the power to force changes to its plan.
The Prime Minister stated she has listened to the concerns of the rebel Tory MPs, but noted future legislation can not hamper the Government's ability to negotiate the final Brexit solution.
Crucially, the motion will be unamendable, meaning MPs can not insert a requirement for Mrs May to go back to the negotiating table, extend the Brexit transition or revoke the UK's withdrawal under Article 50.
One of May's mantras is that "no deal is better than a bad deal" and Brexit campaigners say Britain would lose one of its negotiating tools if the government can not threaten to walk away from the talks, which have all but stalled.
"It's a fight we've got to have and it's best sooner rather than later".