While in Tokyo, Harper and Prime Minister Yoshihiko Noda are expected to formally launch free-trade negotiations.
Government officials say a joint study on areas of economic co-operation showed a number of complimentary areas and Canada has set ambitious goals.
In addition, the Japanese government is expected to relax restrictions on imported Canadian beef.
Japan has the world's third largest economy.
In Bangkok earlier Saturday, the government announced it had set aside $12 million over two years to help detect and prevent human smuggling operations.
Roughly $7 million of the new funding will go toward projects in southeast Asia with Thailand being a major beneficiary.