The Tor short-range air defense system, code-named the SA-15 by NATO, was designed during Soviet times to shoot down aircraft and precision guided weapons.
The arrest came amid anti-government protests in Tehran over the missile blunder. Donald Trump warned Iran against "another massacre" of protesters.
"My message is simple and clear: stop escalation. Exercise maximum restraint. Restart dialogue," UN Secretary-General António Guterres said.
NATO Secretary General Jens Stoltenberg has called a meeting in Brussels to discuss the crisis.
Iran will no longer abide by any of the limits of its 2015 nuclear deal, the country's state television reported on Sunday.