The party suffered heavy losses in a dramatic night which saw its majority at County Hall destroyed, leaving party leaders "in shock".
Independents now form the biggest group, with 26 councillors on the local authority.
Flintshire had been the only remaining Labour-run council in North Wales and local Labour leaders were quick to blame the defeat on national problems and Gordon Brown's government, rather than local issues.
Aaron Shotton, Labour leader on Flintshire Council, said it had been a "very disappointing night", but added that national issues had been at the forefront of voters' minds.
In an exclusive interview, he said: "The Labour group here in Flintshire campaigned on solid, sound policies and I'm proud of that.
"If there are concerns locally we will listen to them and take them on board.
"It is important Westminster does take note of these results and I'm sure it will."
Before yesterday's elections, Labour had a fragile majority at County Hall, occupying exactly half of the 70 seats on the county council.
But their tally was cut to just 22 in a night which saw gains for Independents, the Conservatives and the Liberal Democrats.
The result means the council is now "hung", with no party having overall control.
Negotiations will take place in coming days to form a "rainbow coalition" in which two or more parties are represented.
Labour had been in control of County Hall since 1996.
Among the Labour casualties last night were five members of the council's executive board – Kevin Jones (Bagillt East), Gareth Williams (Buckley Bistre East), David Wilkes (Greenfield) and Ros Griffiths and Derek Butler, who both represented Broughton South.
There were also losses in traditional Labour "heartlands" such as Flint and Deeside.
Of the 22 seats kept by Labour last night, five were uncontested.
In Ewloe, one of the most hotly-contested seats, former Labour AM and deputy chief constable of Merseyside Police Alison Halford was elected as a Conservative candidate.
Labour councillor and Flintshire Council chairman Ann Minshull said: "The results are to do with central government.
"People have said to me they are upset about the abolition of the 10p tax rate – this is something that came over strongly.
"We expected a backlash, but perhaps not quite as severe as it has been. We are in shock."
Antoinette Sandbach, Conservative parliamentary candidate for Delyn, said: "We are absolutely delighted by the results that have seen our presence on Flintshire Council more than double from four to nine councillors.
"The disastrous results for Labour reflect on their total inability to deliver good services and value for money in Flintshire."
The election count took place through the night at Flint Pavilion and ran on until the early hours of this morning.
During the count, a minute's silence was held in memory of Stuart Brown, an independent candidate in the Hope ward who died on Monday.
The election for Hope has been postponed.
It was also announced that Ken Richardson, who lost his seat as Labour councillor for Leeswood, was "seriously ill" and had been rushed to hospital.
For a full list of results from Flintshire CLICK HERE
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