The Czech Republic said it had informed NATO and European Union allies about suspected Russian involvement in the blast, which killed two people, and the matter would be addressed at an EU foreign ministers' meeting on Monday.
The expulsions and allegations by the Czechs have triggered its biggest dispute with Russia since the 1989 end of Communist rule, when Prague was under Moscow's domination for decades.
The incident also poured more fuel on the worst Russian-Western tensions since the Cold War, stirred in part by Russia's military build-up on its Western borders and in Crimea, which Moscow annexed from Ukraine in 2014, after a surge in fighting between government and rebel forces in Ukraine's east.
The Czech Republic kicked out the Russian embassy staff on Saturday after saying investigations had linked Russian intelligence to the blastin the ammunition depot some 300 km (210 miles) east of the capital Prague.
Russia's Foreign Ministry said the Czech accusations were absurd as Prague had previously blamed the blast on the depot owners, and Moscow would hit back hard.
"We will take retaliatory measures that will force the authors of this provocation to fully understand their responsibility for destroying the foundation of normal ties between our countries,” a ministry statement said.
“This hostile move was the continuation of a series of anti-Russian actions undertaken by the Czech Republic in recent years. It’s hard not to see the American trace (here)," it said, accusing Prague of "striving to please the United States against the backdrop of recent U.S. sanctions against Russia".
Czech Interior and acting Foreign Minister Jan Hamacek said on public television investigators believed the 2014 blast was meant to target an arms shipment due to leave the depot, and to occur after it was gone, likely to Bulgaria.
He said police had later identified two suspects as the same Russian military intelligence officers - Alexander Petrov and Ruslan Boshirov - wanted by Britain for the poisoning of former Russian spy Sergei Skripal and his daughter with the nerve agent Novichok in the English city of Salisbury in 2018.
Petrov and Boshirov are believed to be aliases used by the Skripals’ attackers, who remain at large. The Kremlin denied involvement in the incident.
Hamacek said Prague would ask Moscow for assistance in questioning them but did not expect it to cooperate.
The Czech investigative weekly Respekt reported on Saturday that the arms shipment was for a Bulgarian arms trader who was believed to be supplying Ukraine at a time when Russian-backed separatists were fighting Ukrainian government forces in the country's east.
Respekt and Czech public radio named a Bulgarian arms dealer who they said Russian agents had tried and failed to kill. News website Seznamzpravy.cz said the arms shipment may also have been destined for Syrian rebels.
Czech police said they were searching for two men who carried passports in the names of Petrov and Boshirov and were in the Czech Republic in the days before the arms depot blast.
TENSIONS RECALLING COLD WAR
On Sunday, the EU's executive commission confirmed that the Czech row with Russia would be addressed during a previously scheduled EU foreign ministers' video conference on Monday.
The United States and Britain offered full support to the Czech Republic, a NATO ally, in its dispute with Russia.
British Foreign Secretary Dominic Raab said on Twitter the Czechs "have exposed the lengths that the GRU will go to in their attempts to conduct dangerous and malign operations," referring to Russia's military intelligence agency.
The United States imposed sanctions against Russia on Thursday for interfering in last year's U.S. election, cyber hacking, bullying Ukraine and other alleged malign actions, prompting Moscow to retaliate.
The 2014 incident re-surfaced unexpectedly at a time of deep sensitivity for Czech-Russian relations.
The Prague government is planning to open a tender worth billions of euros to build a new nuclear power station, and security services have demanded that Russia's Rosatom be excluded from bids as a security risk.
President Milos Zeman and other senior officials have been arguing for keeping Russia in the bidding, but the chances of that appeared on Sunday to have diminished significantly.
"The probability is very low that Rosatom will participate in the expansion of (nuclear plant) Dukovany," Industry Minister Karel Havlicek, who was previously in favour of including Russia, told Reuters in a text message.