A bill to fund the US government through mid-February has gained the support of enough members of the Senate to win passage and prevent a partial shutdown of federal agencies at the end of this week.

The vote late on Thursday came after some Republican senators threatened to block the process in order to voice their opposition to the Biden administration’s vaccine mandates. Senators voted on an amendment to defund the federal vaccine mandate, which ultimately failed, clearing the way for the passage of the short-term funding bill.

The measure, which was approved by lawmakers in the House earlier in the day, will keep the federal government funded for the next two and a half months.

The need for vaccine mandates, which have been introduced by Joe Biden, has taken on additional importance as the US braces for the impact of the Omicron coronavirus variant.

The plot by Republican senators to undermine the vaccine mandate came after some Republican states have already sought to diminish mandates, by expanding unemployment benefits for employees who have been fired or quit over the requirement to get the vaccine.

On Wednesday, the House Freedom Caucus, a group of rightwing Republicans in the House of Representatives, urged their Senate colleagues to block the funding bill, also known as a continuing resolution, “unless it prohibits funding – in all respects – for the vaccine mandates and enforcement thereof”.

In a letter to Mitch McConnell, the Senate minority leader, the House Freedom Caucus said that the Friday deadline gave their Senate colleagues “important leverage” to prevent funding for mandates.

Biden introduced vaccine mandates, which require employees to be vaccinated or submit to weekly testing, for federal workers and contractors in July. In September, Biden ordered healthcare workers to be vaccinated and companies with 100 workers or more to require Covid-19 vaccines or testing, which the government said would cover more than 100 million employees. Those measures have been put on hold by court rulings, after Republican state attorneys general, conservative groups and trade organizations sued to stop the regulations.