Perennial backlogs of testing coupled with shortages of kits, lack of access to personal protective equipment (PPEs) and surging cases of Covid-19 are derailing containment of the virus.
With widespread community transmission firmly establishing itself in the country, the Ministry of Health says risk communication, laboratory testing and contact tracing are among the key challenges.
But these may not be the only headaches the government is facing.
With the outbreak unlikely to peter out on its own, the key sub-groups of populations spreading the virus also keep changing.
According to the World Health Organization (WHO), the extent of infection in the community by people who never develop symptoms (asymptomatic transmission) remains unknown.
Although there are many unanswered questions about transmission of SARS-CoV-2, experts say symptomless transmission makes Covid-19 far harder to fight.
Health officials dismissed the risk for months, pushing misleading and contradictory claims in the face of mounting evidence.
At the onset of the infection, travellers were quarantined and tested before the focus shifted to truck drivers.
In Kenya, particular clusters of people have been noted to record significantly high cases of infections.
The sub-groups have intermittently been changing from travellers and truck drivers to youth and healthcare workers.
To explain this phenomenon, Dr Eddy Odari, a medical microbiologist, says that initially, the assumption was that the disease was of the affluent and only people who took flights had it and could spread it.
But with international flights suspended, truckers who became the new reservoirs and potential spreaders were forgotten, therefore becoming a bridge of infection from one place to another along their route of travel.
"When the focus was on travellers, truckers were a neglected group. While the government suspended international and cross border travels, there was no measure put in place for the truckers until it was too late," explains Dr Jeanette Dawa, a medical epidemiologist at Washington State University - Global Health Programs, Kenya.
Soon, the youth became the next reservoir.
Young people have been found to be not only asymptomatic but also agile. By moving around, they act as reservoirs of the virus.
Now, frontline healthcare workers are fast becoming the next group of what Dr Odari refers to as the key population, with 670 positive and eight dead from the virus.
Medics face double the risk of getting infected because most of them interact with patients who could be asymptomatic but are seeking other health services, he says.
He added, "Once again we are forgetting about boda boda operators. This is a group of young people who have close contact with passengers, sometimes ferrying two or more people. Given their age, most of them may be infected and asymptomatic."
But with community transmission increasing, focusing on niche groups such as truckers, youths, public transport, or even healthcare workers is not the solution.
"It's normal for this shift to happen with any new disease as we have reached the new phase of community transmission," says Dr Dawa
With limited resources, the government concentrated on the entry points but now that the disease has fully integrated into the community, experts say the strategy must also change.
According to Dr Odari, mapping out regions will better guide response, but concentrating on one group does not mean that others should be abandoned.
"Our testing strategy has to move to targeted testing guided by evidence. For instance, molecular testing should be guided by a serological survey."