The Tory vote fell by more than 2% to 206,950 (13.3%) but the party ended up in more positions of power than five years ago following the local elections on May 3.
The SNP, which polled the most votes, the biggest share at 32.31%, said the growing number of Tory-Labour pacts was a betrayal of voters' intentions.
SNP MSP for South Scotland, Chic Brodie, who represents South Ayrshire, where one of these formal coalitions is in place, said: "For Labour voters across the country the growing number of Tory-Labour pacts in councils across Scotland is a real betrayal of what they voted for.
"Scotland's councils need progressive partnerships to protect people from the Westminster-imposed cuts, not these deals that defy the Labour rhetoric.
"The decision to go into partnership with the party who are cutting disability benefits and refusing to invest in jobs and growth across the country is a kick in the teeth to those people suffering the effects of those Tory cuts and makes a mockery of Labour's claims to stand against the Coalition's cuts agenda.
"Voters in Scotland clearly rejected the Coalition parties, yet Labour is giving them a lifeline when they only won 9% of the councillors in Scotland.
"Labour voters didn't expect their votes would be used to let the Tories in the back door to form council administrations with Labour."
The rise in anti-Nationalist coalitions is only a recent phenomenon as they first began to appear around five years ago.
In Aberdeenshire, the SNP was by far the biggest party, but was shut out of power by a coalition of opponents. In East Dunbartonshire, it was the equal biggest party, but suffered the same fate.
In Midlothian, Labour suffered the same fate, drawing eight each in the battle for seats with the SNP, only to witness the backing of an Independent and tacit support of a Green lock them out of power after generations in office.
In Falkirk, Labour did a deal with two Tories and an Independent to take control.
Leader of the Labour group, Craig Martin, said: "This is great news for Falkirk and great news for Scottish Labour.
"No party won an overall majority here but as the leading group, Labour has secured agreement of other members to lead the council and implement our manifesto.
"Jobs are absolutely key for Falkirk and we need to keep up our programme of regenerating the towns and villages. We will work in partnership with the Scottish Government where possible, but we will not be beholden to them."
The final result of the election came in yesterday from Dunoon, where the poll was delayed because of the death of a candidate.
This allowed the SNP to make a final calculation that they had received 502,864 votes nationally (32.31%) compared to Labour with 488,180 votes (31.37). The Tory vote fell by just over 2% to 206,950 (13.3%).