The Czech Republic and US have said they are "close" to an agreement on the installation of a US missile defence radar in the eastern European country.
Mr Topolanek did not say what the three words in dispute were
Czech PM Mirek Topolanek said there were "only three words remaining to resolve" before a deal could be signed, after talks with President George Bush.
The US wants to build the radar station as part of a global shield against ballistic missiles from "rogue" states.
Earlier, Mr Topolanek said he would not seek Russia's permission for the base.
He said Prague would co-operate with Moscow on many issues, but would decide its internal affairs alone. He also
Russia has said the project will upset the military balance in Europe and warned it could have no choice but to point its own missiles at the installations.
President Vladimir Putin last year compared the plan to the Cuban missile crisis of the 1960s, which saw the US and Soviet Union go to the brink of nuclear war.
After meeting at the White House on Wednesday, Mr Topolanek and President Bush both said they were "close" to reaching an agreement on the hosting of part of the US missile defence shield in the Czech Republic.
"There are only three words remaining to resolve," the Czech prime minister said.
"Sometimes one word matters a lot, and sometimes an agreement might fail because of one word, but this is not the case. These are just minor details, I'm sure we are going to finalize it soon," he added.
Mr Topolanek did not say what the words were, but said the dispute "actually relates to environmental protection and the standards that should be adopted".
Mr Bush said reaching agreement over such issues was complicated, but stressed there was a "will to get it done".
"These aren't easy agreements to put in place," he added.
In a speech at the Heritage Foundation in Washington on Tuesday, Mr Topolanek said the radar would be crucial for his country's security, brushing off criticism from Moscow.
"This is not an issue of one radar installation... it primarily concerns an utterance of free will to defend ourselves," he said.
"Our civilisation will end if we lack the will to defend ourselves," he added.
Mr Topolanek accused Russia of trying to sow confusion among Nato allies, particularly those like the Czech Republic and Poland that were members of the Moscow-dominated Warsaw Pact during the Cold War.
"We do not want to belong again to the sphere of Russian influence. We do not want to belong to a group of countries which have to ask Russia for permission if they want to ensure their own defence."
There is heavy opposition to the radar plan in the Czech parliament and a recent survey of public opinion there found 70% of people opposed to the defence shield, the BBC's Rob Cameron in Prague says.
Earlier this month, Poland and the US reached an agreement in principle to install interceptor missiles on Polish soil.