Senior Conservative MP Ken Clarke has warned there are some Government ministers who are “not excessively fond of workers’ rights” and retaining them after Brexit.

The comments from the former Chancellor came during the second of eight late-night sittings in the Commons on the EU (Withdrawal) Bill – the legislation that aims to transpose EU law onto the UK statue book after Brexit.

But the Government avoided any serious backbench rebellion after five amendments to the bill were voted down by MPs in the Commons on Wednesday evening.

Clause 58 – put forward by the Labour frontbench – sought to ensure that after Britain’s departure from the bloc that EU derived employment rights, environmental protection, health and safety standards and consumer standards can only be amended by primary legislation.

The amendment was defeated by 311 votes 299, giving the Government a slim majority. Just one Conservative rebel, Mr Clarke, voted with Labour for the amendment.

Shadow Brexit minister Matthew Pennycook said his party had put forward the amendment to the bill to prevent secondary legislation being used by future governments to “chip away at rights, entitlements, protections and standards that the public enjoy and wish to retain” after Brexit.

During the debate the former Chancellor and pro-European Conservative asked why, if the Government did not intend to water down workers’ rights after Brexit, ministers were not prepared to enshrine this in the Bill by backing the amendment.

“Heaven forbid by party should swing to the right at any time in its long and distinguished history,” he said.

“There are members of the present Government who are not excessively fond of lizards and bats and or workers' rights, and we could be all reassured if he will undertake to put on the face of the bill reduced formal powers.”

Despite voting with the Government the former Conservative attorney general Dominic Grieve warned that laws protecting such rights will be brought to the “lowest possible status” in Parliament after Brexit.

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Mr Grieve later said he wanted an assurance from Government that the matter was being looked at, also describing Labour's proposed change as having “problems of its own”.

He went on: “I put the Government on notice that we are going to have to draw together the issues that we're debating today, and indeed I'm convinced it will be similar issues next week, all of which derive from the same problem, as to the way the Government has approached this and drafted this legislation at the moment, and it must be remedied.”

On the Government benches, Robert Buckland, the solicitor general told the Commons: “The Brexit process will in no way whatsoever be used to undermine or curtail the rights of workers that have been enshrined both in domestic law and in law by virtue of the EU.”

Mr Buckland added there was an essential clause to preserve the domestic statute book and to provide certainty over what was domestic law. He later later hinted he was prepared to make concessions at report stage following questioning from Mr Grieve and Mr Clarke.

MPs in the Commons also voted down an amendment to the EU Withdrawal Bill put forward by Caroline Lucas by 313 to 295.

The amendment sought to ensure that animals continue to be treated as sentient being after Brexit in domestic law. “The omission in terms of the transferral of this bit of EU law into UK law, I understand the reasons that's it not been able to be directly transposed, but I think it is something that we could very easily rectify,” she told MPs.

“I'm not expecting anyone to find any great controversy about that, I think we're simply saying, and what new clause 30 is simply seeking to do, is to make sure that we close that gap.

“I am not suggesting for a moment that as a result of not closing it we're all suddenly going to go out and start murdering kittens. No one is suggesting anything like that.

“But what we are simply saying is that this is an important protocol.”

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During the debates on the various amendments Priti Patel, who resigned from Government last week following a series of undisclosed meetings with Israeli officials, also made her first speech as a backbench MP since stepping down as International Development Secretary.

She joked about her “intensive course” over the past week on “how to stage an exit” as she backed the Government’s Brexit plans.

“Of course I am speaking today in this debate following an intensive course over the past week, I think it's fair to say, on how to stage an exit which was the focus of a degree of international attention,” she said.

“So for anyone who is still tracking my movements, it's fair to say that I can confirm that as I walked into the chamber this afternoon I passed statues and portraits commemorating some of our greatest statesmen including Margaret Thatcher and Winston Churchill, statesmen who stood up and defended democracy, freedom and sovereignty of our great nation.”

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Referring to the proposed legislation, Ms Patel added: “This Bill paves the way for a smooth withdrawal from the European Union and it complements many of the debates and discussions that have happened, Article 50 and delivers on the will of the British people as expressed in the referendum.”

At Prime Minister’s Questions earlier on Wednesday, Theresa May said the Government was listening to the contributions being made in the debate and “listening carefully to those who wish to improve the Bill”.