Kenya also secured Sh30 billion from the Japan Bank for International Cooperation to purchase heavy machinery and mechanised assets.
The Olkaria Geothermal Development Project will get Sh15 billion. Japan will also provide Sh1 billion for the production of medical oxygen for various hospitals.
Through the United Nations, Kenya will receive Sh320 million in humanitarian aid for those affected by the recent floods caused by El Nino rains.
President Ruto witnessed the signing of the bilateral agreements on Thursday after holding talks with Prime Minister Kishida of Japan.
"After a comprehensive engagement with the Prime Minister on the partnership between Kenya and Japan, I am confident that our bilateral relations will remain strong, robust and dynamic," he said.
Others include a Memorandum of Understanding (MoU) on cooperation in the ICT, health, finance and security sectors.
The head of state said the MoU will include enhancing the capacity of the Kenya Medical Research Institute to build on its pandemic management potential at a cost of Sh3 billion.
To strengthen the partnership between the two countries in defence, an agreement on Defence Cooperation was also signed.
This makes Kenya the first African country to sign a defence pact with Japan.
"This will enable us to work together in promoting peace and stability in Africa and all maritime trade routes," Ruto said.
The President acknowledged Japan's support for the completion of Phase II of the Mwea Irrigation Scheme and the National Rice Masterplan.
"This is a mechanism for achieving food security in our country and, indeed, Africa," he said.
The two leaders also agreed on the modalities of financing national development through frameworks such as government-to-government and Public-Private Partnerships.
"As a consequence, a PPP framework was signed between our two governments. We, therefore, agreed to take deliberate steps to facilitate the private sector to play a leading role in Kenya-Japan economic cooperation programmes and projects," he said.
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The Head of State urged Japan to support reforms of the international financial system that will guarantee developing countries fair and equitable development financing.
"Japan has a strong voice which can support and amplify effectively the disenfranchised voices of developing countries in regard to their peculiar developmental needs in access to affordable financing," he said.
The President acknowledged Japan's support for the UN Secretary-General's budgetary proposal for the modernisation of the United Nations Office in Nairobi.
Ruto also urged Japan to support Kenya's campaign to strengthen UN agencies resident in Nairobi.
"I also appealed to His Excellency the Prime Minister to support our bid to host the International Plastics Convention in Nairobi," he said.
The two leaders discussed the security situation in the Horn of Africa , the Great Lakes region and Haiti .
"I requested Japan's support for the Multinational Stabilisation Mission to Haiti and for other AU regional peace initiatives, particularly those in which Kenya is playing a leading role," he said.
At the same time, Ruto appealed to Japanese investors to invest in Kenya's manufacturing, agriculture and technology sectors.
The President noted that the implementation of the government's Bottom-Up Economic Transformation Agenda has opened up numerous opportunities in the agriculture, manufacturing and technology value chains.
He expressed optimism that the partnership would yield a win-win outcome, granting Japanese companies access to Kenya's highly skilled workforce in need of opportunities.
The Head of State told a Kenya-Japan Business Forum in Tokyo, that the country is poised to be the African workforce hub given its youthful population, with a median age of 20, skills, professionalism and diligence.
"We want your manufacturing exploits in Kenya to have local content and utilise our skilled workforce. In turn, this will create job opportunities for our young people," he said.
He assured that by investing in Kenya, Japanese companies will not only access the Kenyan market, but also the East African Community and the 1.4 billion African market made possible by the African Continental Free Trade Area (AfCFTA) agreement.
President Ruto also told Japanese investors to exploit Kenya's arable land which has the potential to make a significant contribution to global food security.
"Africa, including Kenya, has sufficient arable land to produce food for the growing population of the world," he said.
The Head of State assured that Kenyan laws protect the interests of foreign and local investors.
"Kenya is a democracy and abides by the rule of law, ensuring that foreign and local investments are safe," he said.
He also urged Japanese investors to explore Kenya's potential in renewable energy which is one of the largest renewable energy reserves in solar, wind and geothermal.
"Japanese expertise in green energy technologies is an opportunity for business that is mutually beneficial to our two countries," he said.
Prime Cabinet Secretary Musalia Mudavadi said President Ruto has embarked on an aggressive foreign diplomacy campaign to woo investors.
Japan's Vice Minister for Economy, Trade and Industry Nobuhiro Yoshida said Japanese investors are encouraged by Kenya's business environment.
This, he announced that has motivated them to scale up their investments in the country, citing the Sh15 billion Olkaria geothermal project.
"Kenya's legal environment supports business and we intend to leverage on it," he said.
State Minister for Foreign Affairs Kiyoto Tsuji said Japan is keen on enhancing the partnership with Kenya and transferring skills to Kenyans.
The National Treasury and Nippon Export and Investment Insurance signed an MoU to strengthen cooperation in industrial development, and green growth and promote the business of Japanese companies in Kenya.
Japanese businesses are keen on investing in the energy value chain, especially generation and distribution, telecommunications, infrastructure, ICT and food production.