Harambee Stars' hopes of qualifying for the 2021 Africa Cup of Nations hang in the balance as they went down 2-1 to hosts Comoros at the Malouzini Stadium in Moroni on Sunday.
El Fardou Ben gave the home side the lead in the 21st minute, but Cliff Nyakeya restored parity for Kenya in the 36th minute.
Faiz Mattoir hit the winner for Comoros in the 49th minute and they held out to claim the three points that takes them top of Group with eight points, five ahead of Kenya who remain in third place with three points.
This result leaves Kenya winless in four of her opening group matches in this competition, the team's worst record in the competition in more than two decades.
The outcome also means Kenya has to win her last two matches away to Togo and at home to Egypt to stand a chance of playing in Cameroon.
Mulee made two changes from the team that drew 1-1 against the same opponent in Nairobi last Wednesday.
Lawrence Juma came on for Eric Johanna in midfield, while David Owino 'Calabar' was preferred to Samuel Olwande on the right hand side of defence.
But Stars were playing catch up as early as the 20th minute.
Mottoir easily went past Calabar on the flank and floated in an inviting cross which Mohammed - who was somehow unmarked in Kenya's box - headed home past a hapless Arnold Origi.
Nyakeya then gave Kenya hope. He capitalised on a defensive blunder by the hosts to fire home an equaliser after 36 minutes.
Comoros coach Abdi Abou would have the last laugh as Mottoir turned from provider to scoring the winning goal five minutes after the break.
Masoud Juma and Johanna Omollo had chances to help Kenya snatch a vital point but fluffed them with only the goalkeeper to beat.
Neither did Stars coach Jacob Mulee's substitutes, John Avire and Kenneth Muguna have enough in them to turnaround the game.