"I expect a verdict of not-guilty, as I have said - she is probably a more honest person than I am," the minister told journalists on Monday.
"I don't know whether the trial is a reason why we should stop and do nothing; for example, should I have said that I was afraid about my wife's situation and would not become minister?" he said.
Pavalkis said he had informed Prime Minister Algirdas Butkevičius about the charges against his wife last Friday, adding the matter was not discussed with President Dalia Grybauskaitė.
LNK television said on Sunday that Kaunas prosecutors had asked that Pavalkiene be found guilty in a large-scale fraud case and sentenced to three years in prison.
The verdict is expected on 18 January.
President was not informed
Dainius Pavalkis did not inform President Dalia Grybauskaitė about charges against his wife when he was nominated for the position of education minister, the president's adviser said.
The president sees the new information as very serious, Daiva Ulbinaitė has said.
"The candidate for minister did not provide such information," Ulbinaitė told BNS on Monday. "Such information is very serious."
According to Ulbinaitė, the president did not receive any compromising information about Pavalkis himself.
"The president was not provided with any compromising information about the candidate for minister of education and science. Pursuant to the Law on Corruption Prevention, special services provide information about candidates for ministers," the adviser said.
Prime Minister Algirdas Butkevicius said on Monday he was not aware of charges against Pavalkis wife Edita Pavalkienė when he accepted Pavalkis' candidacy for minister of education and science. The premier now believes the government should wait for the court ruling before taking any action.