On Wednesday, a long-range ballistic missile fell in the Sea of Japan 250 kilometers (155 miles) from Russia's Far East after North Korea was holding missile test launches.
During a Web cast, Putin said, "We would prefer it if Russia and the international community did not receive such presents."
But striking a note of caution, he said "these events should not lead to emotions that would conquer common sense when considering such issues."
He reiterated Russia's position of concern about the incident, which was voiced Wednesday by the Foreign Ministry.
"The tests are being held in a country bordering on Russia and in close vicinity to our borders," Putin said.
He called for talks on North Korea's nuclear problem to be resumed and a compromise sought.