Some 80 percent of primary school teachers and 70 percent of junior high school teachers are working in the countryside, she said.
The higher education reform since 1994 has given college graduates the freedom to choose where they want to work, she said.
And most people want to work in the cities, not the rural areas.
"In China's cities, perhaps 10 graduates are competing for one teaching job. But the rural areas have much harsher living conditions, and therefore it is difficult to attract educated young people," she said.
As some teaching jobs in the countryside are vacant, nearly 400,000 substitute teachers, most of whom may not have the required diploma, are hired to teach at rural schools, according to the ministry.
Not working as regular teachers, they are not included in the statistics about unqualified teachers. So experts say the actual number of unqualified teachers taking posts at schools could be bigger than the official figure.
In recent years, the government has taken measures to improve the quality of teachers in the countryside, including the exchange of teachers between rural and urban schools, training of rural teachers, and recruiting university graduates to work in the countryside.
Between 2006 and 2008, 59,000 university graduates were recruited to work at 6,400 schools in 490 counties. They are paid by the central government.
At least 70,000 university graduates will be recruited to teaching jobs at rural schools this year, Guan said.
The ministry also closed some primary schools and asked students to attend better schools based in a county seat or a populated village, in order to provide them with better teachers and facilities.
But Li Zhiren, a researcher with Chinese Society of Education, told China Daily that the measure has led to some primary school students dropping out of school.
"The young children have to either walk a long distance to school or pay a fee to sleep at school dorms. Some families cannot afford these and had to ask their children to quit school. It is a new problem that the ministry should solve," he said.