A Christian radio station was hijacked late on Tuesday night, and verses from the Qur'an were played.
The radio station cut its broadcast, resuming three hours later in the early hours of Wednesday morning.
A message on the Hope FM Facebook page said that its signal was "interfered with, by a foreign signal".
"To our listeners, Friends of Hope, partners, clients and stakeholders of Hope FM. We take this opportunity to thank you for your overwhelming concern...We assure you that all is being done to ensure we get to the bottom of the matter," the message continued.
"We are indebted to you for the calls, messages, prayers and visits on the matter. And as is our nature, in all things we do give thanks. Romans 8:28."
The station's website says it is "based on a firm Christian foundation," with a vision to see "Kenya and the rest of the world impacted with the Gospel of our Lord Jesus Christ through the transforming power of the Holy Spirit." It is run by the Nairobi Pentecostal Church, and was the site of a petrol bomb attack in 2006, in which a security guard was shot dead and two others suffered gunshot wounds.
The incident occurred soon after a programme discussing Christianity and Islam had been aired, reports said at the time.
Yesterday's hijack follows a number of similar incidents. According to the BBC, the website of Kenya's The Star newspaper was hacked last week, and "terror-related material" was posted.
The Twitter and YouTube accounts for the US military command that oversees operations in the Middle East were also hacked on January 12 by a group claiming to be sympathetic towards the Islamic State.
"American soldiers, we are coming, watch your back, ISIS," the hackers posted on the US Central Command Twitter feed.
On January 11, a Kenyan pastor was shot dead by armed gunmen on motorbikes in Mombasa. The assailants were believed to be part of the extremist group Al-Shabaab, a militant Islamic group from Somalia, which has been active in Kenya.