This was done to simplify red tape blamed for holding up trade in the trading hub of the region.
Kenya is the main trade gateway to east Africa, through its Indian Ocean port of Mombasa, but traders say it takes too long to get goods cleared and permit-related delays ramp up costs.
Previously, entrepreneurs had to fill several forms and visit 24 different government agencies to get the permits and pay the levies, fees, duties and taxes they need to get goods across borders.
Using the new system, traders will no longer need to physically take documents from one agency to another for processing but can now enter all necessary information online.
Speaking at the launch, Kenya's President Uhuru Kenyatta said currently it takes an average of 7 days to clear cargo through the port of Mombasa and about 5 days at Jomo Kenyatta International Airport (JKIA), the regional air hub.
However, the new Kenya National Electronic Single Window System, would hasten the process, he said.
"With the electronic Single Window System in place, we intend to progressively reduce the cargo dwell time at the port of Mombasa to a maximum of 3 days and at the JKIA to one day so as to significantly ease the cost of doing business in the region," he told a gathering that included regional presidents.
Kenyatta said other countries in the region were also planning to adopt the system, and that there was a plan to implement one system to serve the five-member East African Community (EAC) economic bloc.
So far only Rwanda runs such a system, launched in 2012.
A single regional electronic system is in use in the Association of South East Asian Nations, or ASEAN, and East Africa would want to emulate that, Kenyatta said.
Uganda's Yoweri Museveni, Rwanda's Paul Kagame and Tanzania's Prime Minister Mizengo Pinda attended the event.
The countries have met previously and also agreed to revamp an existing railway network from Kenya's port and extend it to Rwanda and also discussed a regional power supply cooperation.
Kenya and Uganda, which have discovered oil, are also considering building an interconnected oil pipeline to a new port being developed on Kenya's northern coast.