Topolanek said the delay related to environmental guidelines for any US presence in his country.
The US says the shield is to protect against the threat posed by states such Iran and North Korea, but the move has angered Russia which sees the installations as a security threat.
"People are wondering 'Is this aimed at Russia? Is this an anti-Russian system?' And the answer is 'of course not,'" the US president said on Wednesday.
"The system we're developing will be able to deal with one, two, or three types of incoming missiles. Russia could overwhelm a system like this," said Bush.
Nato summit
Bush also appeared to indicate that he understood Czech opposition to hosting Russian observers, which has been suggested as part of a plan to ease Moscow's concerns.
Russia has reportedly threatened to target any future base in Poland with its missiles, a move which has sparked concern in Warsaw.
Before leaving for Washington, Topolanek said both the Czech Republic and Poland wanted to finalise plans on the missile shield in time for a Nato summit in Bucharest in April.
The US leader is set to discuss the issue with Donald Tusk, the Polish prime minister, in Washington on March 10.