NASA appeared to be losing vital county seats in the Tuesday polls while Jubilee Party cemented its authority in its strongholds.
Latest provisional results of the contested poll showed Jubilee on a path to retain nearly all governor seats its held after 2013.
NASA lost the Kwale, Nairobi and Machakos seats on what has been attributed to its failure to agree on a single candidate.
The opposition had 26 counties against Jubilee's 21 in the 2013 polls.
In Nairobi, Governor Evans Kidero [ODM] lost to Senator Mike Sonko but the incumbent rejected the results.
Kidero was the senior most NASA politician in Nairobi.
But NASA retained the Mombasa Governor seat through Hassan Joho (ODM). Joho was challenged by Suleiman Shahbal of Jubilee.
Early tallies showed that Nairobi Senator Mike Sonko (Jubilee) won with 824,063 votes (53,48%) against the incumbent's 660 591 votes (42,87%).
In Kwale, Wiper candidate Chirau Mwakwere demanded a repeat of elections which Salim Mvurya was tipped to win.
By press time, Makwere was a distant second with 26, 776 votes (15,97%) against Mvurya's 108 359 votes (64,61%) in more than 540 out of the 612 polling stations.
On the other hand, Bungoma Governor Kenneth Lusaka (Jubilee) trailed his closest rival Wycliffe Wangamati (Ford Kenya) who extended the lead. 172,441 votes (48, 74%).
Jubilee retained its Kiambu seat after Kabate MP Ferdinand Waititu garnered 740,986 votes (78.16%) against 199,293 votes (21.02%).
Jubilee’s Meru county Kiraitu Murungi candidate garnered 271 959 votes (52.15%) to oust Governor Peter Munya with 223,316 votes (42.82%).
In Uasin Gishu, Jackson Mandago is likely to retain his seat with 186,034 votes (57.16%) against Zedekiah Buzeki who got 139,439 votes (42.84%) from 95 per cent of the results tallied for the county.
NASA lost the Machakos Governor Alfred Mutua set an early lead with 239,520 votes (53.31%) against Wavinya Ndeti who had 199,685 votes (44.44%).
In Kirinyaga, Anne Waiguru had 158,760 votes (54.14%) while Martha Karua got 119,410 votes (40.72%).
Joyce Laboso garnered 175,932 votes (67.20%) to unseat Isaac Rutto who got 85,863 votes (32.80%) in Bomet.