The news could cause a stir in Japan, where both the U.S. military presence and its nuclear subs are controversial.
The Houston made calls in March and April in the southern Japanese naval ports of Sasebo and Okinawa.
The ministry said leaked radioactive cooling water was detected during routine maintenance on the Houston in Hawaii in June and it was believed to have posed no threat to humans or the environment.
Sasebo city official Akihiro Yoshida said the government monitoring during the submarine's port calls showed no abnormal increase of radioactivity in the area's waters.
"Still, we are rather concerned," Yoshida said.
The incident comes just weeks ahead of the arrival of the U.S. nuclear-powered aircraft carrier USS George Washington in Yokosuka, just south of Tokyo.
The ship's arrival was originally set for August under a Japan-U.S. security alliance, but is being delayed until late September because of a fire aboard the vessel in May. The George Washington is relieving the soon-to-be decommissioned USS Kitty Hawk and will be the first U.S. Navy nuclear powered vessel to station permanently in Japan.
The George Washington's deployment had already triggered protests and the fire escalated concerns that many Japanese have about nuclear power.
Masahiko Goto, a lawyer representing a citizens' group opposing the George Washington's deployment in Yokosuka, sharply criticized the U.S. Navy for withholding the problem for weeks.
"They had discovered the radiation leak weeks ago and did not inform the Japanese government immediately," he said in a statement. "The U.S. Navy's handling of the accident and lack of transparency showed there is no way we can trust them."
The Foreign Ministry said the U.S. Navy informed them of the leak Friday but waited a day to announce it because the amount was negligible, stirring a flurry of criticism.