"But that's a far cry from helping protesters against the combined might of the Revolutionary Guard, the militias and so on - and the [Iranian] police, who are so far completely unified."
Scowcroft's admission that Washington has agents stationed in Iran comes a day after the US president issued tougher rhetoric against the government in Iran.
Barack Obama's sterner tone came after days of deadly clashes between the opposition and Iranian security forces and militias.
Obama has been criticised by US conservative politicians for not taking a stronger line against Tehran amid the government crackdown, but Scowcroft, a former adviser to presidents Gerald Ford and the senior George Bush, said the US could only do so much.
"We don't control Iran. We don't control the government, obviously," he said.
"There is little we can do to change the situation domestically in Iran right now and I think an attempt to change it is more likely to be turned against us and against the people who are demonstrating for more freedom.
"Therefore, I think we need to look at what we can do best, which is to try to influence Iranian behaviour in the region."
At least 19 people have been killed in post-election violence in Iran, which broke out at the scene of protests questioning the veracity of the poll results.
Mir Hossein Mousavi, the main challenger to Ahmadinejad, has rejected the official results of the vote and has called for a fresh election to be held, while Mehdi Karoubi, another defeated candidate in the election, has called the new government "illegitimate".
But the Guardian Council, Iran's highest legislative body, has said that there were no incidences of major fraud in the vote and has declared that the official results will stand.