The Russian foreign ministry said the footage screened last night had caused "an extremely negative" reaction among officials and accused the broadcaster of "supporting terrorists."
The ministry had originally asked Channel 4 not to broadcast the interview saying it would allow Basayev's "views and threats to get out to a wider audience" but Channel 4 refused to back down because of the negative consequences and propaganda victory for the terrorists.
In a statement, the broadcaster said: "We recognise, of course, that Shamil Basayev's views will be regarded as widely repugnant, but we reject utterly any notion that we are being irresponsible.
"It is simply not the case that the running of such material can be equated with condoning it. This has also been the case for many other instances where the views of those who advocate terrorism, including Osama Bin Laden, have been carried out by the broadcast media."
Russia has a $10m (£6m) bounty on Basayev, who claimed responsibility for the Beslan school siege last year and the Moscow theatre siege in October 2002 where 700 people were taken hostage.
In the interview, Besayev said his original intention was to seize several schools in Moscow and St Petersburg, rather than just Beslan, but he ran out of money.
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