Hundreds of heads could have their pay docked for participating in the Sats boycott, a move that would undermine relationships between school leaders and local authorities "for many years", a union has warned.
Emma Knights, chief executive of the National Governors' Association, said substantial numbers of councils were putting pressure on school governing bodies to dock money from heads taking part in the industrial action.
A TES survey of more than half of England's local authorities suggests that at least 4,000 primary schools refused to administer the key stage 2 tests this week.
Mick Brookes, general secretary of heads' union the NAHT, wrote to local authority directors of children's services this week praising them for their "measured response" to the boycott so far.
But he urged them to "question their motivation" if they seek to punish heads through sanctions that could include docking pay and disciplinary proceedings.
"I believe this attitude will sour relations between the local authority and my colleagues for many years at a time when it is even more important, especially for my colleagues in the primary sector, to maintain strong and positive links with your officers," he wrote.
His letter came as dozens of local authorities contacted school governors about how to respond to the boycott, including providing advice on how to dock the pay of participating heads.
Their advice is in line with national guidance from the Local Government Employers organisation.
Ms Knights said that heads who had withdrawn their labour had to accept there would be consequences.
"Employers aren't trying to be awkward, difficult or petty," she said. "It (the action) is a consequence of (them) taking action. It's a completely valid option, it's perfectly legal and it would not be unreasonable."
She said that docking pay would be the "more standard procedure". However, despite pressure from local authorities, final decisions on sanctions will be made by governors and many will choose not to enforce them, Ms Knights conceded.
The amounts deducted could range from a "nominal" cut to half or a full day's pay, depending on the amount of contracted work heads had failed to fulfil.
The law states that the amount deducted should be "proportionate", but the rest is left to governors' discretion.
Advice from the National Employers' Organisation for School Teachers, which represents children's services departments, says that governing bodies should be made aware that they could face challenges in the courts from auditors if they fail to deduct pay.
This is because failing to make a deduction would appear to "condone industrial action", which is in breach of their statutory duty.
Meanwhile, it emerged this week that ministerial calls for governors and local authorities to bring in alternative staff to administer Sats tests went largely unheeded.
Ms Knights said concerns over the legality of former schools secretary Ed Balls' proposals had meant "next to no" governing bodies had acted on ministers' advice.
The level of participation in the boycott left academics split on whether it would render league tables for this year useless.
Stephen Gorard, professor of education at Birmingham University, said tables could still be published, but that there would need to be a "really clear warning if there appears to be a large increase or decrease" in results.
See News, pages 24-25
BOYCOTT BY NUMBERS
600,000: pupils due to sit key stage 2 Sats this week
16,000: approximate number of English primary schools with Year 6 pupils
4,000: minimum number of schools which took part in the boycott, according to TES poll
7,213: number of NAHT and NUT members who voted in favour of a boycott
72: percentage of pupils achieving level 4 or above in 2009 English and maths Sats.