"My decisions were finalised after people's attitudes became clear," Putin said.
"We weren't prepared for such a turn of events. To tell you the truth, we could imagine how people felt but did not know for sure."
"Only after conducting the first sociological surveys, which, to tell you the truth, were done in secret, the numbers were pretty close to reality," he said while meeting with supporters of the All-Russian Popular Front, a group at the forefront of his re-election campaign in 2012.
Later "when the process began to develop" at the referendum on March 16, "this figure grew more to nearly 97 percent," he said.
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"That is an amazing figure," he added.
Putin gave no details of when the secret polls were was held, or who conducted it.
Pro-Russian figures seized government buildings in Crimea in late February, at roughly the same time as well-armed soldiers appeared on the peninsula, surrounding Ukrainian military bases and manning government buildings.
Crimea and the city of Sevastopol were proclaimed Russia's two new regions after the referendum, which was condemned by Western powers as illegitimate.