The United Nations Children's Fund (UNICEF) says up to 50,000 children in the impoverished southern African country are in need of anti-retroviral therapy (ART).
According to Shaba, official reports show that 26-30,000 children a year have been infected with HIV since 2004, mainly through mother-to-child transmission.
"These are reports of children we have been getting since 2004 ... not all children need treatment now, but the government is serious now to reverse the situation and we have intensified the prevention of mother-to-child transmission of HIV," she said.
She said government now had 144 delivery and service centres, up from 36 in 2004, throughout the nation's 28-districts to help stem transmission.
"We are getting dividends...we should be getting a different situation within one to two years," she added.
In 2005, UNICEF estimated there were some 83,000 children living with HIV, while close to a million children had been orphaned by AIDS.
The pandemic has cut life expectancy to 36 in Malawi, where some 14 percent of the country's 12 million population are infected with HIV, which claims the lives of some 80,000 people a year.
A free ARt programme launched in 2004 now provides some 110,000 adults with treatment.