The two-thirds majority needed in three provinces to defeat the constitution will now be counted from all registered – as opposed to actual – voters.
On Sunday Shia and Kurdish members of parliament pushed through the changes in the referendum rules on 15 October.
Sunni Arabs reacted angrily to the amendments on Monday.
They believed many registered voters may not show up at the polls because of violence.
“We have expressed our position to the national assembly and to the leadership of the government,” said Jose Aranaz, a legal adviser to the UN electoral team in Iraq.
Mr Aranaz said parliament’s decision was unacceptable and would not meet international standards.