Anne-Marie Trevelyan had been due to attend a meeting of the International Trade Committee on Wednesday morning.
But she pulled out the night before ahead of an expected statement in the House of Commons on steel tariffs later on Wednesday.
Committee chair Angus Brendan MacNeil said the committee was "unanimous" in its "disappointment" and felt it set "a very worrying precedent" for "the way the government is dealing with scrutiny of the free trade agreements".
He added: "We feel that this is a disrespect to the committee. We are very disappointed."
A spokesperson for the Department for International Trade said Trevelyan had informed MacNeil that she could not attend on Tuesday night, apologised and offered an alternative two-hour slot next week.
The spokesperson said: "The International Trade Secretary is in the process of finalising a finely balanced decision on the steel safeguard by June 30.
"This is an issue of national strategic importance and she has had to make sure she is able to review the final advice from the department before updating Parliament today."
They added: "We have made enhanced commitments to scrutiny and transparency at every stage of UK-Australia negotiations.
"This includes ministers appearing in front of the ITC and giving Parliament over six months to scrutinise the legal text, in addition to the 21-day period provided by us triggering the Constitutional Reform and Governance Act process."
Earlier on Wednesday, the committee had published a report urging the government to delay ratifying the Australia deal to allow greater scrutiny by MPs.
The deal has been heralded by the government as the first negotiated from scratch since leaving the EU amid a promise that it would leave the country STG2.3 billion better off.
But the government's attitude to parliamentary scrutiny of that deal, the committee's report claimed, "has undermined that statutory process and shown great discourtesy to Parliament".
MacNeil said that they had been "consistently hindered" in attempts to fully examine the deal.
This is not the first time the committee has intervened to accuse Trevelyan of dodging questions on the free trade deal, signed in December last year.
International agreements must be brought before parliament, with 21 sitting days allocated to MPs to consider any deal.
That process was triggered earlier this month by the government, and the trade committee has accused the government of repeatedly frustrating efforts at effective scrutiny of the new and complex trade deal.
In the report, MPs bemoan a "persistent lack of clarity" in the timetable for parliamentary scrutiny, calling their demands for a guaranteed period of time to complete their report "not unreasonable".
"Overhasty ratification, without the chance to complete full scrutiny, runs the risk that any significant disbenefits of the Agreement may be overlooked or disregarded," MPs wrote in the report.
MacNeil said it was "vital" that MPs were able to properly scrutinise the deal and questioned the apparent need for urgency.
"Given that ministers are keen to extol the virtues of this deal, it is beyond belief that the Government is so eager to rush it through without appropriate scrutiny, especially considering that the Australian government is not rushing to ratify on their side.
