Grim developments in Iraq, including the kidnapping of seven Chinese on the eve of Cheney's visit to Beijing on Tuesday, threaten to overshadow Cheney's week-long trip to Asia.
In a brief session with US embassy staff before meeting Koizumi, Cheney hailed the state of US-Japanese relations and "the growth in our cooperation" on economic and security matters.
Cheney is one of the key US officials behind the Iraq invasion. He has kept a low profile since arriving in Tokyo at the weekend.
The hostage incidents have greatly complicated Cheney's visit to the region, putting him on the defensive and overshadowing economic issues and efforts to eliminate North Korea's nuclear weapons programme.
Officials travelling with the vice president in Japan said the US government was playing a role behind-the-scenes - both on the ground in Iraq and through other channels - to help free the Japanese hostages.
"He (Cheney) remains in close contact with the White House and other senior administration officials. We are monitoring closely the developments in Iraq and elsewhere," said Cheney spokesman Kevin Kellems.
"He (Cheney) remains in close contact with the White House and other senior administration officials"
spokesman, Dick Cheney
In his meeting with Koizumi, Cheney was to deliver a message of appreciation for Japan's commitment of manpower and money to the Iraq operation, his aides said.
He will also tell the Japanese leader that Washington is committed to a 30 June deadline for transferring sovereignty to Iraqis despite renewed violence.
In addition to Iraq, Cheney is expected to press Japan to reopen its markets to US beef, banned three months ago because of the first US case of mad cow disease.
In Beijing, he is expected to discuss thorny currency policy and market-access disputes.
A senior administration official said ending North Korea's nuclear programme would also be "an important subject not only in Beijing, but also in Tokyo and Seoul."
Cheney will visit Seoul from Thursday as part of his trip, postponed last year because of the start of the Iraq invasion.