The two leaders spoke on the phone for 35 minutes on Thursday morning, a day after North Korea launched a ballistic missile towards the Sea of Japan, public broadcaster NHK reported.
During the conversation, Abe and Trump also stressed that China has a key role in persuading North Korea to put an end to its missile and nuclear weapons programmes.
Their conversation comes as Trump prepares for his first bilateral meeting with his Chinese counterpart Xi Jinping on Thursday and Friday, reports Efe news.
Abe said that he told Trump that Japan is paying close attention to how China handles the issue of North Korea.
"(We) agreed that yesterday's missile launch by North Korea was a dangerous act and a grave threat to (Japan's) security," added Abe.
North Korea has stepped up its weapons programme since Kim Jong-un assumed power five years ago, conducting a record number of nuclear and missile tests in 2016, and underscoring his regime's decision to use nuclear deterrence to ensure its survival.