Mr Kiraithe said handover of the SGR, which is one of the issues raised by the Kenyan staff, would be done in three phases.
"It will be done in three, five and fully in 10 years," he told journalists in the capital Nairobi.
Mr Kiraithe said the government took the first batch of Kenyans for training in China in preparation of the handover of Madaraka Express.
The government has asked Kenyans to “bear with the Chinese” who are facing accusations of racism and discrimination in the running of the Standard Gauge Railway.
Government spokesperson Eric Kiraithe on Wednesday said Kenyans, including those facing maltreatment, should “appreciate the work” the Chinese are doing.
The China Road and Bridge Corporation, the builder and operator of the line, stands accused of discriminating Kenyan workers— who are expected to take over the running of the rail service in 10 years— in unemployment, assignments, salary, sitting arrangement, catering and personal hygiene services among others.
But without giving details, Mr Kiraithe said the Uhuru Kenyatta administration had put in place “systems” to resolve issues surrounding the operations of Madaraka Express passenger service and the cargo train.
He downplayed allegations of mistreatment but added that investigations into the claims were ongoing.
Instead of painting the multi-billion-shilling project in bad light, the spokesman said, Kenyan staff should expose the specific individuals who allegedly mistreated them.
"We have put all measures to deal with these issues, but if you are a Kenyan who claim to have mistreated and you have not reported to police and have not reported to Fida, then you have to," Mr Kiraithe told journalists in the capital Nairobi.
And while acknowledging that the government had received some complaints on racism, he said action will be taken against foreigners found culpable of discriminating against locals.
Mr Kiraithe blamed unnamed persons, accusing them of being as detractors who are out to slow down the Vision 2030 flagship project.