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Senator Peter Harder waits to be officially welcomed to the Senate on Parliament Hill in Ottawa in April, 2016. Mr. Harder, the Liberal government's point man in the chamber, is tasked with making it a more impartial.Adrian Wyld/The Canadian Press

The Senate has backed down in its budget bill feud with the House of Commons, but it also sent a message to MPs that it isn't happy about it.

In a 50-33 vote, the Senate agreed not to insist on its amendments to the government's budget bill. However it sent a message to the House of Commons restating its right to amend any legislation it wishes.

Conservative senators opposed the motion and said the vote proves their belief that Prime Minister Justin Trudeau's independent Senate appointments are actually Liberals in disguise.

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"Clearly, we've seen in the last few days, Trudeau's appointments are doing what is expected of Senators when they get appointed by a certain prime minister. They support his agenda and that is what they are doing in this particular case. The voting patterns have shown that," said Conservative Senator Leo Housakos. "It's unfortunate that the independent Liberal senators who clearly were insulted by the behaviour of the government unanimously caved."

The vote brings to an end the uncertainty surrounding the fate of Finance Minister Bill Morneau's sweeping budget bill. At more than 300 pages, the omnibus legislation will enact changes to the powers of Parliamentary Budget Officer, allow a $35-billion Canada Infrastructure Bank to move ahead, launch a new office called the Invest in Canada Hub and change the way Parliament reviews government borrowing.

After a Senate effort to remove the infrastructure bank provisions failed Monday in a 38-38 vote, the Senate focused on another controversial aspect of the legislation. The bill includes a 2-per-cent increase to the excise tax on beer, wine and spirits and sets future annual increases in in line with inflation.

The Senate voted Tuesday to approve amendments that removed the so-called escalator tax on alcohol. The House of Commons passed a motion unanimously on Wednesday that rejected the Senate amendments as an infringement on the privileges of the House of Commons.

Senators objected to that language, stating that the Senate has a long history of amending financial legislation.

The motion approved Thursday by the Senate stated that the Senate does not insist on its budget bill amendments, "But that the Senate confirms its privileges, immunities and powers as provided under the Constitution to amend legislation, whatever its nature or source, and that a message be sent to the House of Commons to acquaint that House accordingly."

Independent Senator Elaine McCoy, who leads a caucus of independent MPs called the Independent Senators Group, said the alcohol tax issue was not significant enough for the Senate to insist on its amendments. She said the Senate sets a high bar for when it would insist on its position in a dispute with the House of Commons.

"We are appointed. We give them our advice. We do not insist on it. Unless it's a very, very important matter, like going to war," she said. Ms. McCoy pointed out that the Senate has amended 20 per cent of government bills over the past year, which is much higher than in the past.

"That is an activist Senate," she said.

How well have the Trudeau Liberals met their legislative goals? John Ibbitson argues there is still a lot left undone that was promised during the election campaign, and the government lags what Stephen Harper had achieved by the same point of his time governing as a majority.