The new agreement also aims to double the number of Aborigines and Torres Strait Islanders employed at the university.

Staff passed the new agreement 706 votes to 73 on Thursday, securing a pay rise of 3.9 per cent in 2013 and a further 3 per cent increase in January.

Despite the increases, National Tertiary Education Union ACT secretary Stephen Darwin said there had been several losses. ''We are disappointed with parts of the agreement,'' he said.

''On balance, we recommended members vote for it because the university was not willing to negotiate further.''

As well as the agreement's pledge to double the number of Aborigines and Torres Strait Islanders employed at the university it will provide leave to staff who are victims of domestic violence.

Mr Darwin said the initiatives were proposed by the union and it was a win to have them included.

Deputy vice-chancellor and lead negotiator Nick Klomp described the deal as good news for the entire faculty. ''There is always more that management wants and probably always more that staff want,'' he said.

''I think on balance, this is good.''

Professor Klomp said the agreement, which follows year of negotiations with staff and unions, also secured the university's position in the top quarter of university pay grades.

In addition to the increases, university management will implement a scheme bestowing annual bonuses of $1000 to $2500 to all staff members, except senior managers.