Hamas was also once an Assad ally but last year endorsed the revolt against him in a shift that deprived the Syrian leader of an important Sunni Muslim supporter in the Arab world.
"Our relations with Iran were affected both on the political and the financial levels," said Ghazi Hamad, deputy minister of foreign affairs in the Hamas-run government in the Gaza Strip.
Hamad declined to provide any figures for the amount of aid Hamas receives from Iran or give details of any cutbacks, other than to say "it did not get to the point of boycott (from Tehran)."
"We have stood by the Syrian people and we have backed the demands of the revolution," Hamad told reporters, saying those positions had led to a worsening of ties with Tehran.
A diplomatic source in the region said Iran has provided Hamas with up to $20 million a month to help pay the salaries of nearly half of 50,000 Gaza government employees.
Hamad said Hamas was still meeting its payroll and "had lots of other sources" of money. But, he added, "Things are not easy ... and we are trying to overcome the problem."
Iran has also provided Hamas with weapons, including long-range rockets that it has used to strike cities deep inside Israel.
Hamad made no mention of any change in Iranian arms supplies to the group, which is boycotted by the West over its refusal to renounce violence, recognize Israel and accept existing Israeli-Palestinian interim peace deals.
On Monday, Hamas urged the Lebanese militant group Hezbollah to withdraw its forces from Syria, where they are battling on Assad's behalf.
The call marked a further deterioration in relations between Hamas and Hezbollah, two long-time allies who have each fought against Israel and advocate its destruction.
"We are with Hezbollah in their resistance against Israel but we are not in favor of their position in Syria," Hamad said.
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