The government on Thursday shut down proposed changes that would ensure less water is returned to the environment in the southern part of the crucial river system.

It was less than 24 hours after the five Nationals senators received a Senate drubbing on the same amendments to a government bill establishing a basin inspector-general.

Leader of the House Peter Dutton gagged debate on Nationals whip Damian Drum's amendments, avoiding Nationals cabinet ministers including reinstalled leader Barnaby Joyce having to vote.

The proposed changes to the basin plan would have also banned the government buying water from irrigators and stopped further environmental flows after 2024.

Government Senate leader Simon Birmingham denied he was angry with the Nationals.

"I don't think there was an expectation that they were going to win. And so people can interpret that however they wish," he told the ABC.

Labor's water spokeswoman Terri Butler savaged the government for the bizarre scenes in parliament.

"It is absolute chaos and the people who will suffer will be the people who rely on the Murray-Darling Basin," she told MPs.

"The people who rely on the health of the rivers. That's all Australians because the Murray-Darling Basin is of incredible economic significance to our country."

Outspoken Nationals senator Matt Canavan said suggestions of a major split in the government were dramatic and over the top.

"God forbid we have a debate in our nation's parliament," he told ABC radio.

"We're at our best and healthiest when we do stand up for our independent causes and issues but we do come together to pass things like the bill last night that went through."

The bill, which also boosted compliance in the basin, took almost two years to come to parliament after the "basin cop" role was announced in 2019.

While the government blamed states for the delay, Senator Canavan said his colleagues flagged amendments well before this week when Barnaby Joyce returned as deputy prime minister.

"The problem is last time we did give them a heads-up they just pulled the bill and we couldn't even do it," he said.

Prime Minister Scott Morrison is being urged to strip the water portfolio from the Nationals when a ministerial reshuffle is announced.

Victorian Bridget McKenzie, who led the charge on the amendments, has been tipped for a return to cabinet with reports she's keen on becoming water minister.

But government Senate leader Simon Birmingham poured cold water on the idea.

"I don't think that's likely, but that's a matter for the prime minister and deputy prime minister to talk through," he told the ABC.

Senator Canavan said he saw no reason for his party to lose responsibility for water.

Australian Associated Press