Liberal Senator David Fawcett has apologised after stating the Labor Party "brought the fleas" and was now attempting to "nitpick" in senate estimates with questions over refugee and asylum seeker policy.

The remark prompted condemnation, with some seeing the senator as branding asylum seekers as fleas.

In a late-night statement, Senator Fawcett said he had been contacted by a number of community representatives who had told him how hurt people had been by the comment.

"Whilst it was never my intention that my comments would refer to refugees in such a way, it’s clear that my poor choice of words has caused hurt to many people, and consequently I sincerely apologise," Senator Fawcett said.

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The apology came after an earlier statement which attempted to defend and clarify the remark.

"I used a figure of speech to describe the Labor party's pursuit of very small detail in the processes within the Department of Immigration and Border Protection and that has been somehow construed by the media to indicate that I have called refugees fleas. That is completely untrue," he said.

He said his comment was a response to Labor Senator Kim Carr's line of questioning, which was critical of the Immigration Department's handling of contracts on Nauru and Manus Island.

"The metaphor was that if they were nitpicking, they were responsible for the cause of that irritation. It's certainly not intended to apply to people who are refugees."

Mr Fawcett's remark followed comments from Liberal Senator Michaelia Cash highlighting large numbers of "unauthorised arrivals" under the preceding Labor government.

Senator Fawcett's colleague, Senator Ian Macdonald echoed Senator Fawcett's comments, describing them as "nicely put".

Labor immigration spokesman Shayne Neumann called for Senator Fawcett to "start treating Australia's humanitarian program with the respect and seriousness it deserves".

"It is beyond belief that a Turnbull Government senator would ever refer to vulnerable people seeking asylum as fleas, and even worse, to have other Coalition senators laugh, cheer and eagerly agree," he said.