The Equality Bill has passed through its final stages in parliament and will now become law after receiving royal assent.

The bill, which gives new protections to gay people, was sent for royal assent last night.

It is designed to consolidate and simplify existing equality laws, encompassing characteristics such as race, gender and sexual orientation.

A flagship feature of the bill is equality duty on all public bodies, which will require institutions such as schools, councils and the NHS to actively promote equality.

Employers will be permitted to use positive action to select candidates from under-represented groups when two people applying for a job have the same qualifications.

The bill will also prohibit private members’ clubs from discriminating against members or guests based on their sexual orientation or gender reassignment and introduce the concept of “dual discrimination”, where people can show they were discriminated because, for example, they are both gay and of an ethnic minority.

An amendment added last month will allow gay couples to have their civil partnerships in church.

However, the bill has been criticised by gay groups, opposition politicians and secular groups for a number of “grey areas”.

One contentious issue is harassment protection for gay people, which critics say does not exist in the bill. The government has said gay people are already protected from harassment due to direct discrimination laws and that there was a duty for schools to continue the existing ban on discrimination.

Trans campaigners argue that there is not enough protection for the many people who live as the opposite gender but have chosen not to seek medical treatment.

The government said last month it would not continue to fight the House of Lords over an amendment clarifying who churches can refuse employment to.

Provisions in the bill would have clarified the law requiring churches only to discriminate in terms of sexual orientation when hiring those who will teach doctrine or lead worship.

But after the Pope publicly criticised the bill, equality minister Harriet Harman backed down. She is thought to have made the climbdown to avoid a continuing dispute with church leaders.

The new laws will begin to take effect in the autumn. The public sector equality duty will be introduced in April 2011, while provisions to ban age discrimination and force companies to reveal pay packets will come into force in 2012 and 2013 respectively.