The possible "strategic treaty" between the United States and Afghanistan is against peace, stability and security in Afghanistan and the region, Foreign Ministry Spokesman Ramin Mehmanparast said in a statement, Press TV reported.
The Iranian official also stressed that the deal would complicate the situation in Afghanistan and the region.
Mehmanparast also urged the Afghan government and nation to be cautious about interference by foreigners in their country's internal affairs.
The United States reportedly plans to set up permanent bases in the country to keep US troops in Afghanistan beyond the 2014 withdrawal deadline.
Afghan President Hamid Karzai has not given a date for finalizing the deal with Washington, but said any long-term partnership would need to be approved by the parliament.
If an agreement is reached on permanent bases, US troops will remain on Afghan soil beyond the planned transfer of security responsibilities by the end of 2014.
The decade-long war in Afghanistan has become more unpopular due to the rising death toll among both Afghan civilians and US-led foreign forces.
The US currently has about 100,000 troops in Afghanistan. The total number of coalition forces in the country is 150,000.
Iran warns against US-Afghan treaty
The possible "strategic treaty" between the United States and Afghanistan is against peace, stability and security in Afghanistan and the region.
