The minister's statement marks the first occasion where Mozambique's government has released the number of teacher deaths due to HIV/Aids.
The education ministry estimates that about 19,200 teachers and more than 100 senior education officials will die of Aids this decade.
The schooling of children living in rural areas of the country has been hit hardest by the Aids pandemic, with one teacher often having to educate more than 100 pupils in a class.
The education ministry recommends that school classes contain a maximum of 35 pupils.
About 16 per cent of Mozambique's 19 million people are infected with HIV, the virus that causes Aids.
The government has installed HIV-prevention programmes in schools and hospitals and set up a literacy programme, but critics say such campaigns are poorly organised.
It plans to employ an extra 9,000 teachers by 2010 and is aiming to set up additional education training programmes.
Aly said Mozambique's life-expectancy rate has dropped to 35 - among the lowest in the world - due to the prevalence of HIV/Aids in the southern African country.
More than 25.8 million people live with HIV in sub-Saharan Africa, 60 per cent of the global total, according to Unaids, the joint UN programme on Hiv/Aids.
The UN programme says that HIV levels appear to be rising in Mozambique.
It estimates that 3.2 million people in the region became newly infected in 2005, with 2.4 million adults and children dying from Aids.
Aly said: "Aids has left a whole generation of pupils without teachers."