The motion was put forward by Labor, however the Opposition and crossbench objected to the issue being referred to the Legislation Committee, which is dominated by government senators.

One Nation Senator Malcolm Roberts said FMD was a clear and present threat, and his party wanted "an inquiry, not a cover up".

"This was originally referred to the government-controlled Legislative Committee, why else would they do that unless the intent was to cover up?" Senator Roberts said.

In the spirit of collaboration, Labor agreed to refer the issue to the References Committee, where the Opposition holds the majority.

Senator Raff Ciccone, who put forward the motion, said the current debate on FMD had undermined the confidence of consumers.

"Farmers expect their elected representatives to work together to keep foot-and-mouth disease out of Australia, not undermine confidence in our ability to keep the agriculture industry foot-and-mouth disease free," Senator Ciccone said.

The Nationals put forward their own motion to refer Australia's biosecurity regime to the same committee, however withdrew when assured the committee would also investigate adjacent biosecurity matters, such as the Varroa mite outbreak in NSW.

"The government's attempt to mark its own homework on their flat-footed response to the FMD outbreak has rightly been rejected by the Opposition and crossbench," Nationals Senator Bridget McKenzie said.

"I welcome Labor's backflip and look forward to the committee freely engaging with industry and experts in order to understand what went wrong as we all seek to safeguard Australia's enviable FMD disease-free status."

Nationals leader David Littleproud slammed the government's response as "too late".

"It took them four weeks to roll out the foot mats, they only just got them in and have allowed thousands of people to waltz through," Mr Littleproud said.

"They should have already banned passengers from bringing back foot items from Indonesia."

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Agriculture Minister Murray Watt said despite the Indonesian FMD outbreak beginning under the former government's watch, the Coalition had only taken an interest in Opposition to "fan the flames".

"When this outbreak reached Indonesia on May 9, what did the former agriculture minister Mr Littleproud do?" Senator Murray asked the Senate.

"Did he introduce foot mats? No. Did he establish biosecurity zones? No. He sent a tweet, that was the only thing he did at the time, and then he didn't say anything until July 6.

"This government has done more on biosecurity in 9 weeks than the Opposition did in 9 years."

Mr Murray said the inquiry was an "excellent outcome" for the agriculture industry.

"After a decade of neglect by the Coalition, this is an opportunity to make sure Australia's biosecurity systems are well prepared to handle the increasing number of threats on our doorstep."

The committee will be required to report its findings by October 10.