The Federal Government has been embarrassed by a procedural bungle in Parliament, after accidentally endorsing a bill amended by Labor, which criticised the Government.

Minister for Revenue and Financial Services Kelly O'Dwyer was seeking to pass the International Tax Agreements Amendment Bill 2016 through the House of Representatives on Wednesday.

But Ms O'Dwyer accidentally endorsed a second reading amendment put forward by shadow assistant treasurer Andrew Leigh.

The amendment calls on the Government "to explain why it has failed to close tax loopholes and increase transparency in Australia".

After some confusion, Ms O'Dwyer appeared to support the amendment, facilitating its passage through the House of Representatives.

Manager of opposition business Tony Burke said it was the first time in the history of federal parliament that a second reading amendment had ever been supported.

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"There has never been a more chaotic government, there has never been a more chaotic parliament and there has never been a leader of the house that has had to endure humiliation from his colleagues on such a regular basis," Mr Burke told Parliament.

"We've only been sitting 10 days, this is not a one-off mistake.

"If the first 10 days are any guide at all, then this is a government that's not counting up its days, this is a government in countdown."

Leader of the House Christopher Pyne described the mistake as an "inadvertent error".

"I would make the point that there are several owners of this error, and I am not going to criticise them individually because it's wrong to criticise the people who work for us, the people who are sitting in the chair," Mr Pyne told Parliament.

"There was a series of events that led to this outcome, and it's a pity."

The Federal Government, with the cooperation of Labor, was able to rectify the mistake and pass the original bill through the House of Representatives, without Dr Leigh's amendment.

The Coalition lost a number of procedural votes in the House of Representatives last month when a number of senior ministers left Parliament early.