The government has clarified that the new e-passport will still be issued after the August 31 deadline.
In a statement, the Immigration Department maintained that the old-generation travel document will no longer be used after August 31, 2019.
Kenyans have been queuing as early as 3am at the Immigration headquarters in Nairobi's Nyayo House in a process that has now become a nightmare for thousands of applicants.
But the government now says it is all because of a misunderstanding.
"The long queues witnessed is due to a misconception that people will not be allowed to apply for the e-passport after the end of August. These are the fears we as Government want to allay," the statement signed by the department's Director General Alex Muteshi said.
The government last week opened four new immigration centres in the country, and six others in the diaspora, in a bid to ease congestion at the Immigration headquarters.
Besides Nairobi, other centres are in Kisii, Embu, Eldoret and Nakuru.
Mr Muteshi said the centres are expected to serve at least 1,500 people daily.
Centres outside the country are Johannesburg in South Africa, Berlin, London and Paris in Europe and Washington DC in the US and Dubai.
In 2017, the government started phasing out the old passports, with holders required to change to new digital passports.
The old documents will become obsolete starting September 1, 2019.