Mr Salmond told listeners: "I'm well on the record as never having approved of either Margaret Thatcher's social or economic policies - that's clear if you look at the interview."
And in a statement after the radio show, he added: "I was commenting on why Scots in particular were so deeply resentful of Margaret Thatcher, and I strongly believe that her social message of 'no such thing as society' and the poll tax cut against the grain of Scotland's social conscience.
"That doesn't mean that the nation liked her economic policies - just that we liked her social policies even less."
He said his views were clear from the full text of the interview.
Labour claimed Mr Salmond's phone call was a sign of "utter desperation".
Labour MSP John Park said: "The first minister doth protest too much.
He added: "The screech of the first minister going into reverse gear can't disguise the own goal he's scored with his praise of Thatcherism. He clearly realised that his off-the-cuff remarks have backfired."
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