Jan Fischer said his country is "ready to participate" in the new plan, which focuses on short- and medium-range interceptors after meeting with U.S. Vice President Joe Biden Friday.
Last month, the Obama administration to base a missile defense shield in Eastern Europe designed to shoot down long-range missiles that might be fired from Iran or other nations.
Biden said Washington would send a team of experts to Prague next month for discussions.
The vice president has been touring Central Europe this week in an attempt to shore up broad support for the reworked missile defense plan and reassure critics that Washington remains committed to guaranteeing the country's security.
The decision has sparked fears in formerly communist Eastern Europe that Washington was sacrificing its interests in order to improve ties with Russia.
On Wednesday, Poland on to the revamped U.S. missile shield.
But in the Czech Republic, biting comments from former but still influential political figures tainted the atmosphere ahead of Biden's arrival.
Biden "should clearly explain the reasons that led the Obama administration to its decision not to build a radar in the Czech Republic," Former Prime Minister Mirek Topolanek said in a statement prior to the vice president's arrival..
Topolanek, whose government signed treaties with the Bush administration to build the radar system and took a lot of heat from a majority of Czechs who opposed the plan, said the Obama administration's moves toward Russia raise questions about "whether the United States is stepping back from the region of Central and Eastern Europe in exchange for better relations with Russia."
Former Czech President Vaclav Havel told the U.S.-funded Radio Free Europe/Radio Liberty that he expected Biden to "make it clear that America is interested in us, that someone else has not pushed us out of America's field of vision."
Analysts, meanwhile, said it was unlikely Biden would leave with a clear commitment from Prague, since the country's weak caretaker government lacks a mandate to move forward on any strategic defense issues, including missile defense deals. A new government will be formed only after general elections in May.
The country has been in political limbo since Topolanek's government lost a parliamentary no-confidence vote in March, just before President Barack Obama visited Prague.
"This government could hardly negotiate anything concrete," said Pavel Prikryl, an analyst at Prague's Association for International Affairs.
Meanwhile, NATO's top official said the alliance welcomes the revamped missile defense plans in Europe and hopes to bring it fully into NATO.
NATO Secretary-General Anders Fogh Rasmussen said the system President Barack Obama envisions, which is meant to defend the West against future threats from countries like Iran, would provide Europeans and Americans with protection against a "real threat."
He spoke to reporters Friday after U.S. Secretary Robert Gates briefed NATO defense ministers on Mr. Obama's plan to reconfigure the Bush-era missile defense system.
Fogh Rasmussen said NATO will work with the U.S. to incorporate the system fully into NATO.