Former prime minister Mr Odinga blamed president Uhuru Kenyatta's Jubilee party for the alleged hacking of the election database.
According to official figures, Kenyatta leads with 54.3 percent votes while Odinga is behind with 44.8 percent votes.
"Hacking was attempted but did not succeed", election commission chairman Wafula Chebukati told a news conference. Under election rules, the Form 34A is used to tabulate results at the polling stations.
All the observers spoke with Odinga and his National Super Alliance (NASA) party to formally express their grievances to the electoral commission and seek redress from the courts if they are not satisfied with the response they get.
Kenyan police opened fire Wednesday to disperse riots and protests in several areas after presidential candidate Raila Odinga made allegations of election fraud.
Former US Secretary of State John Kerry, leading an observer team from the Carter Centre, expressed confidence in the integrity of the system, introduced in a bid to avoid fraud in a country prone to post-poll violence. Uhuru must go home.
"Our election management system is secure.
We noted these efforts were directed at ensuring sufficient transparency in the presence of party agents that were at numerous polling stations", said Mahama.
On Tuesday, general elections were held in Kenya.
Alleging vote-rigging, he also brought up the unsolved torture and murder of a top election official just over a week before the vote. In 2007, Odinga claimed that the vote had been rigged in favor of then-incumbent Mwai Kibaki, who was declared the victor.
Kura Yangu Sauti Yangu, a set of rights groups coordinated by the Kenya Human Rights Commission, commented on the situation via a statement, saying that the voting had been orderly, but that early results were "completely unverifiable".
The first incident occurred when protesters at the Mathare slums in capital Nairobi blocked traffic by lighting bonfires on the streets.
In 2007, the disputed election led to two months of ethnically-driven political violence that killed almost 1,100 people and displaced 600,000 others. The commission said that verifying and confirming of election returns were ongoing and that they have received over 40,000 form 34As.