Detectives on Monday confiscated thousands of heroin sachets in Mathare, Nairobi.
John Musyoka, 37, was arrested during the raid as one suspect fled.
A Toyota Axio was also detained and police are hunting for the other suspect.
Musyoka will be arraigned on Tuesday.
The arrests comes days after four Tanzania cousins were jailed.
They were accused of trafficking 4.3kg heroin worth Sh13 million to Hong Kong through Jomo Kenyatta International Airport.
The four were also fined Sh1 million each.
Twayba Hashim, Tina Martin, Omary Saidi and Rehema Ramadhan were arrested on March 2014.
