Foreign Minister Gamini Lakshman Peiris said the government had told Ban's chief representative Neil Buhne that the days of protests outside the main UN office in Colombo would end on Friday.
"Given that background, the UN secretary-general acted in haste by asking Mr Buhne to come to New York," Peiris told parliament, adding that his government "regretted" the move.
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The UN Development Programme's regional centre in Colombo has been virtually under siege since Tuesday from demonstrators demanding that Ban halt a UN probe into alleged rights abuses during the final stages of Sri Lanka's civil war.
The protests have been led by Housing Minister Wimal Weerawansa, who has begun what he says will be a hunger strike to the death outside the UN compound.
Weerawansa said Friday he was resigning his cabinet seat to deflect criticism that his agitation was being orchestrated by the government.
"I have no intention of causing embarrassment for the government," he said in a letter to Preside