The Westminster Government will “totally respect” the result of the ballot on September 18, Alexander said.
He responded to claims that impossible demands in any post-referendum negotiations would not be met and that the “status quo” would be the default option.
“What I would say is that the policy of the UK Government is and has been clear,” Mr Alexander told BBC Scotland’s Good Morning Scotland programme.
“We totally respect the right of people in Scotland who will vote in the referendum in September to make their decision.
“The result of the referendum will be respected, full stop, end of story.”
Scotland’s First Minister Alex Salmond demanded clarity in light of the reported comments from an unnamed senior coalition source.
“It seems to suggest a senior coalition source, in terms of taking this arrogant assumption so far, is suggesting they somehow won’t accept the result now in September,” he told the programme.
Such an approach would be against the spirit of the so-called Edinburgh agreement signed by the First Minister and Prime Minister David Cameron to pave the way for a legally binding referendum, he said.
The source reportedly said: “A Yes vote in the referendum would be the start of a process, not the end of one; we would start negotiations. But if Alex Salmond made impossible demands, we would not just roll over and agree to everything he wanted. If we could not reach agreement, the status quo would be the default option.”