Elaine Ann Knowles, formerly head of Bromborough Pool primary in the Wirral, was accused of disregarding exam guidelines by allowing 15 key stage 2 pupils to look at their papers again.
Teachers Gill Charvill and Sue Johnson saw Mrs Knowles calling the pupils in individually after the test on May 13, 2002, after taking the unsealed papers to her office.
Mrs Johnson said: "The headteacher told me she was making sure that the children had the answers in the right box.
"I knew that this was not allowed but I was not aware of how serious it was as I thought she was just ensuring the answers were in the right place rather than changing them.
"It was my view that Mrs Knowles wanted the children to give their best possible account of themselves in the test even if that meant breaking the rules."
Mrs Charvill told the panel she thought all 15 pupils in the KS2 class were called out of her lesson to see Mrs Knowles after the tests.
Mrs Knowles has also been charged with failing to follow proper procedures on declaring pecuniary or personal interests and to charge a pre-school previously attached to the school for the services of her staff.
The GTC, sitting in Birmingham this week, also heard that she failed to issue staff with job descriptions, did not follow procedures for performance management and did not carry out regular pay reviews after starting at the school in 1994.
Mrs Knowles, 50, also faced claims, which her representative denied, that she failed to give Mrs Charvill and Mrs Johnson a formal salary review.
The hearing was adjourned to a later date.