The party suffered losses in Wakefield, Sheffield and Hull, despite holding onto all three councils, on a night when the Conservatives comfortably saw off the party’s challenge in several flagship London boroughs.
But the party gained control of Kirklees council, winning three seats to take an overall majority, and moved closer to power in neighbouring Calderdale after gaining an extra seat.
In Leeds, Labour tightened its grip on the city council, despite losing some seats to the Tories and independent groups.
It saw its majority increase in Bradford, while in North East Lincolnshire the party will have a reduced majority despite gaining seats, as the Conservatives enjoyed a successful night.
Several councils in Yorkshire will not announce their results until later today, with the result of the Sheffield City Region mayoral election expected this afternoon.
Jonathan Carr-West, chief executive of the Logal Government Information Unit, said: “It looks like a better night for the Conservatives than many would have anticipated, while Labour results have not quite lived up to expectations.
“In London, Labour were targeting flagship Conservative councils like Wandsworth and Westminster but have fallen short despite increasing their number of seats.”
In Hull, Labour retained control but the Liberal Democrats confounded expectations by winning seven seats.
The unexpected surge by the Lib Dems shaved Labour’s majority to just five in a night of high drama which also saw Hull’s first Asian councillor elected.
In Sheffield, where the council’s ruling Labour group has suffered heavy criticism over its controversial tree-felling programme, Labour lost four seats, including two to the Liberal Democrats and two to the Greens, but gained a seat from the struggling Ukip.
And in Wakefield, the Conservatives made gains by winning seats in Horbury and South Ossett ward, Ossett, Wakefield Rural and Wrenthorpe and Outwood West.
Reflecting on the result, Wakefield’s Labour council leader Peter Box said: “It’s been a mixed night. It’s clear that the UKIP vote has gone to the Conservatives.”
Describing the turnout as “very, very disappointing”, he added: “I think people have got election fatigue and I think also there is a slight disenfranchment with politicians generally”.
In Bradford, the Labour Party gained four seats, going from 48 to 52, well above the 46 needed for a majority. Council leader Susan Hinchcliffe told the Telegraph and Argus newspaper: “I’m pleased with the gains we’ve made, but we obviously still have a lot of hard work ahead and I’m keen to get on with that as quickly as possible.”
Labour managed to remain the largest party in the North East Lincolnshire council by a handful of votes. The party picked up two seats, while the Conservatives gained three.
In a night of many gains and losses at the Leeds count, several seats changed hands, but Labour ultimately gained three seats overall.
The Tories also gained three seats. But it was a bad night for the Lib Dems, who lost three seats overall despite taking one from Labour in Rothwell.
Perhaps the most stunning victory of the night was that of the Garforth and Swillington Independents, which was originally made up of two councillors who defected from Labour last year amid a flurry of claims and counterclaims.
Former cabinet member Mark Dobson and his two fellow candidates delivered huge numbers to wipe out Labour in the area.
In the capital, Jeremy Corbyn’s party had made a significant push to take Tory “crown jewel” authorities but failed to make the strides needed.
The Tories retained control of Wandsworth Council, last won by Labour in 1974, after winning more than half the seats, as well as Westminster City Council.
The leader of Kensington and Chelsea Labour group conceded the party would not take overall control of the local council, which under the Tories faced a furious backlash over its handling of the Grenfell Tower tragedy.