The agreements were reached during the visit to Tokyo of Venezuelan President Hugo Chavez.
They include plans to explore for new oil sources in Venezuela's Orinoco belt, develop a new natural gas field and fund the upgrading of refineries.
Venezuela has some of the world's largest oil and gas reserves but the oil price drop has hit financing.
Japanese Prime Minister Taro Aso and Mr Chavez agreed to set up a working team to explore the possibility of the development of oil at Venezuela's Orinoco oil belt and liquefied natural gas, as well as funding for the operations, Japanese foreign ministry officials said.
Energy allies
The two countries aim to become "energy allies", with Venezuela hoping to eventually supply Japan with one million barrels of oil per day, Mr Chavez was quoted as saying by Venezuela's state-run Bolivarian News Agency, or ABN.
The president said Japanese companies could also be involved in railway projects, housing and highway construction in Venezuela.
State-affiliate Japan Oil, Gas and Metals National Corporation, Inpex Corporation and Mitsubishi Corporation will pursue a joint feasibility study with Venezuela on the Orinoco oil belt in the next two years, Venezuela's Energy Secretary Rafael Ramirez said at a signing ceremony in Tokyo.
Venezuela also agreed with four Japanese trading houses - Mitsubishi, Itochu, Mitsui & Co and Marubeni - to begin participating in the development of a gas field for liquefied natural gas, said Mr Ramirez, who is also the head of the state oil company, Petroleos de Venezuela SA.
If realised, it could allow much of the LNG to be brought over to Japan beyond 2013, he said.
Separately, Venezuela signed a memorandum of understanding with Japan Bank of International Cooperation, Mitsubishi and Itochu for loans totalling $1.5bn (£1bn) to finance the upgrade of two refineries.
This follows a credit line of $3.5bn opened in 2007.
The two nations have enjoyed diplomatic relations for 70 years. Mr Chavez last visited Japan in 1999, the year he took office. He and Mr Aso were reported to have discussed baseball before getting down to business.
