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The time has arrived to withdraw South African peacekeeping and protection unit troops from Burundi, Defence Minister Mosiuoa Lekota said on Monday.

"We (will) try to get out of there now. We think we have done what we could," he told reporters in Pretoria.

The first priority was securing the withdrawal of the 369-strong protection unit, which has been guarding the safety of Burundian leaders during peace talks leading to the country's political transition.

He would start negotiations this week to achieve that, the minister said.

As for the 1266 South African peacekeeping troops deployed in Burundi under a United Nations mandate, Lekota differed from the UN's assessment that they should stay a while longer.

"The UN continues to have a sense that they would like to allow for a period of time to see there is stabilisation and that the stability is sustained for a period of time.

"We think actually that the atmosphere is so positive now that we can withdraw.

"Unfortunately, the mission of the UN can only be decided upon by the UN. The protection unit was our deployment and that we can take a decision on."

Lekota said the South African deployment was instrumental in achieving a democratic dispensation for Burundi.

The SANDF, which was the first to deploy troops in that country, has gained valuable peacekeeping experience, he added.

Former rebel chief Pierre Nkurunziza, a Hutu, was sworn in as Burundi's first post-transition president last month following national elections which began in June.

In terms of the country's new constitution, the government comprises of 60 percent Hutus and 40 percent Tutsis.

Burundi's conflict, which has claimed an estimated 300,000 lives, erupted 12 years ago when the country's first democratically elected president, a member of the Hutu majority, was assassinated by the Tutsi-dominated military.

The country's sole remaining rebel group, the National Liberation Forces, has not endorsed a peace deal and has continued attacks on the government.