The House of Lords has voted through the government’s Health and Social Care Bill at its second reading, defeating motions to place sections under greater scrutiny or stop it in its tracks altogether.

Peers this afternoon voted down an amendment proposed by crossbencher Lord Owen, to set up a special committee to examine the proposals for changes to the duty of the secretary of state for health, by 330 votes to 262.

The bill will now pass to the committee stage, where Lords will review the legislation line by line.

Another motion put forward by Labour Lord Rea, which would have effectively “killed” the bill by preventing it getting a second reading, was defeated by 354 votes to 220.

The votes followed a two-day debate involving more than 100 peers.

Although Lord Rea’s amendment was widely expected to fail, the fate of Lord Owen’s had been more uncertain, with negotiations between Labour, Conservative and crossbench peers continuing until the final moments before the votes took place.

Earl Howe had objected to setting up a committee as it could delay the passage of the bill through parliament, which he warned could prove “fatal” to the reform plans.

This was despite assurances from Lord Owen that his amendment was not a “blocking motion”, and shadow leader of the house Baroness Royal gave her word that the bill would leave the Lords by mid-January.

But Lord Ashdown, former leader of the Liberal Democrats, told the house he could not understand how scrutiny of the bill would have been improved by setting up a special committee.

Today’s vote does not mean that further changes cannot be made to the bill. Earl Howe told the Lords this afternoon that the secretary of state would be responsible and accountable for a comprehensive health service. “If there is an amendment which will improve the bill, we will make it.”

He also said ministers would table a new duty for the secretary of state regarding education and training during the committee stage.

The government is also considering how foundation trusts can be required to explain how their income from private patients is benefiting NHS patients.

Earl Howe also confirmed that after the bill is written into law, post-legislative scrutiny will take place within three years, sooner than the normal five.