Nato members have expressed "grave concern" over Russia's threat to suspend participation in an arms treaty limiting conventional forces in Europe.
Mr De Hoop Scheffer was speaking at Nato talks in Oslo
Nato Secretary General Jaap de Hoop Scheffer said the agreement was one of the cornerstones of European security.
Earlier, President Vladimir Putin said Russia should halt its compliance with the treaty because of concerns over US plans for a missile shield in Europe.
The US secretary of state said Moscow should respect its treaty obligations.
Condoleezza Rice also dismissed Russia's concerns over the US missile shield as "ludicrous".
The 1990 Conventional Forces in Europe (CFE) treaty limits key offensive weapons like tanks, artillery pieces and aircraft across the continent.
The CFE was adapted in 1999 after the collapse of the Warsaw Pact.
'Disappointment and regret'
Mr Putin made the threat during his annual address to parliament, saying that Russia would suspend implementing the CFE until all Nato members had ratified it.
Nato states have not yet ratified the new version, first demanding the withdrawal of Russian forces from Georgia and Moldova.
Mr Putin also accused the Nato of exploiting the situation to increase their military presence near Russia's borders.
The Russian leader appeared to have linked his threat with US plans to put elements of a new missile defence system in Poland and the Czech Republic.
The US wants to station 10 interceptor missiles in Poland, with radar operations in the Czech Republic.
Reacting to Mr Putin's comments at a Nato meeting in Oslo, Mr De Hoop Scheffer said: "That message was met by concern, grave concern, disappointment and regret."
He was speaking during the first of two days of talks of Nato foreign ministers, which was dominated by President's Putin speech and the debate over the US missile shield.
Mr De Hoop Scheffer's comment represents a serious repost, the BBC's diplomatic correspondent Jonathan Marcus says.
He says it is unclear where this dispute is heading, however some analysts believe that President Putin largely has a domestic audience in mind.
But the row is souring the atmosphere at a time when the US needs Russia's help in advancing peace in the Middle East, rolling back North Korea's nuclear programme, and above all persuading Iran to abandon its plans for uranium enrichment, our correspondent says.