"If this had happened under me, I would have tried not to let it happen," he said in an interview with Russian television on Wednesday, calling the events in Crimea "a pain and a tragedy that is very hard to agree with".
Yanukovych was ousted following a series of massive protests after he decided to scrap an agreement with the European Union in favor of closer ties with Russia.
With a new, pro-European administration in Kiev, Crimea's largely Russian-speaking residents voted in March to become part of Russia, in a hastily organized referendum held as Russian troops patrolled the region.
Speaking from exile from the southern Russian city of Rostov-on-Don, Ukraine's former president said the poll had taken place in a "protest mood".
He said the annexation of the peninsula, where Russia's Black Sea fleet is based, was "due to the current rulers of Ukraine", accusing them of hostility towards Russian-speaking Ukrainians.
"It is their radical position on the Russian language, to those territories where the Russian-speaking population lives," Yanukovych said in an interview broadcast by independent broadcaster TV Rain.
"The attempt to dictate to them how to live led to people living in those regions speaking out in protest," he said.
He said he could not accept Ukraine's break-up and feared further crises in eastern and southern regions where Russian speakers are concentrated.
"How can I as president of the country see the country falling apart? Those processes that are happening now in the east and south of Ukraine, they also need to be taken very seriously," he said.
Yanukovych fled Kiev in late February. The parliament has since passed a resolution that he failed to fulfil his duties as president.
Russian President Vladimir Putin has said he still considers Yanukovych the legitimate president of Ukraine, but dismissed him as having no political future.
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