The Children's Laureate and woman behind the Gruffalo books said the laudable aims of the Curriculum for Excellence (CfE) sometimes got in the way of good teaching.
School staff are expected to link what is learned to four underlying principles: that pupils be successful learners, confident individuals, responsible citizens and effective contributors.
Donaldson, a former secondary teacher who lives in Bearsden, told The Herald: "It is good that we have these criteria and they are really good aims for schools, but teachers should be freer to get on with it.
"I have a friend who teaches in a special-needs school and there is a child there who can hardly move, but if they manage to push a ball along the teacher will have to equate that to one of these outcomes, rather than recording what they did.
"If a child is whimsical and chatty, but very interested in foxes, on their report card teachers cannot say, 'loves foxes, but I wish she wouldn't chat so much', they have to say she could be a more responsible citizen.
"I feel sorry for teachers having to toe the line and tick the boxes, because my impression of those I have met is almost universally they are doing a great job."
The other self-confessed bee in her bonnet is what she calls the "pendulum" swinging from one reading technique to another.
She said: "When my children were at primary school in the 1980s, phonics was almost a dirty word. The 'look and say' technique being used instead was fine, and many children learned to read by that method, but for many it was a case of 'look and guess' and children did not learn how to decode words.
"I was pleased when phonics made a return, but the pendulum seems to be going the other way, where phonics is becoming much more rigid. It is important to use a blend of techniques."
Donaldson's concerns have prompted her to launch a series of short plays with other well-known authors, designed to help improve reading skills.
The Bug Club Plays To Read, published by Pearson, includes dramas about modern children as well as new versions of traditional tales, including a rhyming version of The Hare And The Tortoise, adapted by Donaldson.
"When my own children were in primary school they used to get parents to visit to hear the children read and they would have reading groups," she said.
"There are still reading groups, but it may be that they are reading different books and are at different stages of the book and it is not very satisfactory because it means other members of the group are bored and restless.
"Reading a play is a way of involving everyone and it is brilliant because it means the children can all take part and can have roles which reflect their reading abilities.
"They know they need to keep up because they have to come in at a certain time, so they also improving at silent reading.
"A play is also something you can read again and again because you can give pupils different parts."
A Scottish Government spokesman said: "Curriculum for Excellence will provide our young people with an education fit for the future. It is the most significant reform of education in a generation and has benefitted from eight years of investment, effort and consultation with teachers, parents, and pupils."