His comments are tantamount to recognition that Russia, which this week said it had withdrawn its last troops from the wrecked republic, has emerged the loser from a 21-month war in which many tens of thousands of lives were lost.
For President Boris Yeltsin, they are also a reminder of one of his nastier political wounds which comes as he is sidelined by illness yet again - this time by a bout of pneumonia, which has wrecked his plans for a bounce- back after his multiple coronary bypass operation two months ago.
According to Russian news agencies, Mr Primakov told a cabinet meeting that there was a "real danger that Chechnya will secede from Russia both de facto and de jure". He added that Moscow must work to prevent, or at least to cushion, such a development.
His warning is likely to fuel the indignation of those in the upper echelons of Moscow's political and military circles who regard Russia's peace accord with the Chechens as a humiliating capitulation. Under the August accord, both sides agreed to postpone a settlement on the republic's status until 2001. In the meantime, they planned to maintain a state of "constructive ambiguity" on their fundamental disagreements over the issue, setting it to one side rather than allowing the deal to founder.
Mr Primakov's warning contradicts that strategy. Elaborate preparations are under way for elections in the Caucasus republic on 27 January; the five top candidates are separatists.
His comments were not his only broadside aimed at the recalcitrant outer edges of the former Soviet empire. He also called for the cabinet to impose economic sanctions on former Soviet republics whom Moscow accuses of discriminating against ethnic Russians living on their territory, in particular Estonia.
Meanwhile, the President's aides were busy trying to contain concerns over his health following Wednesday's revelation that - a fortnight after returning to work following heart surgery - Mr Yeltsin had developed pneumonia and was back in the Central Clinical Hospital in Moscow.
The Kremlin was at pains to emphasise that his ailment was not related to his recent surgery; that his temperature was normal, and that he was being treated with antibiotics. They indicated he was even managing to work - holding, for example, a 15-minute conversation with the Prime Minister, Viktor Chernomyrdin.
Although such explanations received a generally sympathetic hearing in wintry Moscow, where 60,000 have fallen victim to a flu epidemic, they did not deter his chief opponent, the sacked national security adviser, Alexander Lebed, from continuing to attack. The retired general - who intends to run for the presidency - spent the day rumbling to reporters about Russia's "rudderless" condition and "power vacuum" .