Iran has railed against US sanctions imposed on 10 citizens and a tech firm accused of cyber attacks on at least 320 universities worldwide, along with US firms and government agencies.
Tehran called the sanctions a gimmick that was provocative, illegal and unjustified.
The Mabna Institute is accused of stealing 31 terabytes of "valuable intellectual property and data".
Iranian foreign ministry spokesperson Bahram Qassemi said the new US sanctions were an act of provocation, and that the move would not prevent Iran's technological progress.
"The US will definitely not benefit from the sanctions gimmick, aimed at stopping or preventing the scientific growth of the Iranian people," Mr Qassemi said in a statement.
The Mabna Institute was established in 2013, and US prosecutors believe it was designed to help Iranian research organisations steal information.
It is accused of carrying out cyber attacks on 144 US universities, and at least 176 universities in 21 other countries, including the UK, Germany, Canada, Israel and Japan.
By targeting the email accounts of more than 100,000 professors worldwide, the hackers compromised about 8,000 of them, according to the justice department.
The two founders of the Mabna Institute are among those sanctioned and their assets are subject to US seizure, a statement by the US Treasury Department said.
The indicted individuals are still in Iran. They were called "fugitives of justice" by US Deputy Attorney General Rod Rosenstein, and could face extradition in more than 100 countries if they travelled outside Iran.
Many of the "intrusions", Mr Rosenstein said, were done "at the behest of the Iranian government and, specifically, the Iranian Revolutionary Guard Corps".
The hackers also targeted the US Department of Labor, Federal Energy Regulatory Commission and the United Nations, according to prosecutors.
Mr Qassemi said the sanctions were an example of Washington's hostility towards the Iranian nation.
Washington has adopted a much more belligerent stance against the Islamic Republic since US President Donald Trump took office in January 2017.