Bomb threat at US Supreme Court ahead of inauguration
Kaveh Lotfolah Afrasiabi was arrested at his home near Boston on Monday, and charged the day after, the US Department of Justice said.
"America's action is a clear hostage-taking of Iranian nationals," Iran's foreign ministry spokesman Saeed Khatibzadeh was quoted as saying by ISNA.
"Americans have sadly become addicted to such actions and take hostages for any excuse," he added.
He called Afrasiabi a "well-known university lecturer" and said the charges against him were "baseless".
Afrasiabi was accused of "acting and conspiring to act as an unregistered agent" of the Iranian government, the US justice department said in a statement.
His website says he had taught at Boston University. He had also been a visiting scholar at Harvard 30 years ago and at Berkeley in 2000-2001.
Read more: Turkey's rise and Iran's decline in the South Caucasus
He has written numerous books, including on the Iran nuclear agreement, and has frequently been quoted by international media.
Afrasiabi faces up to 10 years in prison if convicted.
Khatibzadeh expressed hope the incoming administration of US President-elect Joe Biden would "distance itself" from President Donald Trump's "hostage-taking approach".
Afrasiabi's arrest comes days after US media reported that Iranian authorities had convicted Iranian-American businessman Emad Sharqi on spying charges.
Iran and the United States have engaged in several prisoner swaps in recent years.
Wednesday also marks the 40th anniversary of the release of 52 American hostages held for 444 days at the former US embassy in Tehran, following the Islamic revolution that toppled the pro-US regime of the Shah.
The United States severed diplomatic relations with Iran in 1980.