"Japan for its part lodged a stern protest with the North Korean side through embassy channels (in Beijing)," Foreign Minister Fumio Kishida told reporters.
He added, however, that there would be no change in the official talks scheduled for Tuesday in Beijing.
The meeting is aimed at checking progress in Pyongyang's promised investigation into the fate of Japanese citizens abducted by North Korean agents during the Cold War.
A South Korean defence ministry official said the North fired two ballistic missiles into the Sea of Japan (East Sea) from its east coast. Both landed in international waters, he said.
"At the government-level consultations, we want to raise the (missile) issue resolutely," Kishida said.
"Although the meeting is where we deal with the abduction issue, we also think it can be an important opportunity to take up missile and nuclear issues as well."
The meeting will be held nearly a month after Tokyo announced it would ease sanctions against Pyongyang if the secretive state reinvestigated the abduction cases, an issue that conservative Prime Minister Shinzo Abe has worked for years to solve.
Japan has said the investigation must be substantive and credible before it lifts its unilateral sanctions.
North Korea admitted in 2002 that it had kidnapped 13 Japanese citizens in the 1970s and 1980s to train its spies in Japanese language and customs.
Five of the abductees returned home but Pyongyang said -- without producing credible evidence -- that the eight others had died, provoking an uproar in Japan.
Pyongyang's reluctance to come clean on the abduction cases, along with its missile and nuclear arms programmes, has derailed talks between the two countries to normalise ties.