The closure followed attacks on two private educational institutions.
Students believed to belong to the All Nepal National Independent Students Union-Revolutionary stormed into Lord Buddha educational foundation college, doused 20 computers with kerosene and set fire to them.
At Thames business school, computers, a photocopier, a fax machine and furniture were destroyed and petrol bombs were exploded.
Both attacks occurred without warning and were carried out by a group of 15-20 students chanting slogans. There were no casualties.
"There is no doubt that these attacks were a warning to schools to close," said the principal of a well-known private school in the valley who did not want to be named.
His school was approached on the same day. "I was told to close. Two men came to my school with a letter that said we should support them by closing down for two days on the following Monday and Tuesday. Exactly what we were supporting was not clear. It simply said, 'Support us in our fight against the corrupt regime.'" At other schools, small groups of men distributed leaflets to children in the playgrounds and to staff and then instructed the school to close.
On the Monday morning, the playgrounds were silent. "I am convinced I would have been attacked if I had remained open," said the principal. "There are people watching all over the place. I have children boarding here and I was afraid that their play would attract attention. I was very scared."
It is a measure of the Maoists' grip on Nepal that their orders are now obeyed without question, even in the relatively unscathed Kathmandu Valley.
It is not only the lost days of schooling that are worrying teachers. They see attitudes changing, too. "All of this is having an effect on the children," said the principal. "They have become very cynical about authority.
"They see that it does not amount to much in the face of threats of violence. They see that education is something that can be messed around with and, as a result, they value it less."