Iain Duncan Smith said a chapter was closed
He told the Tories' Scottish conference in Perth that the move helped contribute to the party's ultimate defeat.
Mr Duncan Smith also told delegates that the Conservatives were not rejected without reason at the 1997 General Election.
Mr Duncan Smith's keynote speech on the final day of the conference earned a standing ovation from delegates.
He said there was "strong evidence" that the tide was turning for the Tories in Scotland after spending a long time on the back foot.
He said that the party's focus on the economy had saved the UK from "economic melt-down" in the 1980s and 1990s.
But he said: "We were not rejected perhaps without reason in '97.
'Things are changing'
"People had not only become bored with us, but Scottish people in particular, I feel, felt that we did not share their concerns and their values.
"The introduction of the poll tax in Scotland a year ahead of the rest of Britain encapsulated the problem, perhaps, for after all perception matters - but things are changing.
"A difficult chapter in recent Conservative Party history may be most associated with Scotland, but it is a closed chapter."
The poll tax, or Community Charge, was introduced in Scotland on 1 April 1989 and then introduced south of the border a year later.
It led to a mass non-payment campaign in Scotland and riots in London before finally being abolished in 1993.
Mr Duncan Smith also said the Tories were now "the party of new ideas" and were once again ready to challenge for power.
He promised that his party's new commitment to help the poor, first outlined following a tour of Glasgow's Easterhouse estate, was not "a passing phase".
He said that only Scotland's Tories could deliver real action against crime, to improve schools and cut waiting times.
'Deserves trust'
"Scottish Conservatives are from Scotland, of Scotland and for Scotland.
"We are the only alternative to the socialists, the separatists and the cynical Liberal Democrats," he said.
And he added: "Now is our opportunity to show the Scottish people that the Conservative and Unionist Party deserves their trust again.
"It is a challenge to us all, and a challenge we must and we will rise to."