Kai Eide said the arrests had completely stopped a channel of secret communications with the UN.
Mr Eide confirmed publicly for the first time that his secret contacts with senior Taliban members had begun a year ago.
Pakistani officials insist the arrests were not an attempt to spoil talks.
However, Mr Eide said the timing was not a coincidence.
'The effect of (the arrests), in total, certainly, was negative on our possibilities to continue the political process that we saw as so necessary at that particular juncture,' he said.
'The Pakistanis did not play the role they should have played. They must have known about this,' he added.
Mr Eide stepped down from his position as UN representative in Afghanistan earlier this month after two years in the post which saw violence escalate and the UN role in fraud-tainted elections mired in controversy.
