Microsoft was fined 280.
5 million euros the equivalent of A$477.2 million, for flouting the order.
The new fine comes on top of the record A$845.6 million fine it already paid in 2004.
It also faces new penalties of A$5.1 million a day which will begin at the end of this month unless the codes are handed over.
“More than two years after the decision … Microsoft has still not put an end to its illegal conduct,” said EU Competition Commissioner Neelie Kroes.
“I have no alternative but to levy penalty payments for this continued compliance. No company is above the law,” Ms Kroes said.
Microsoft, which earned A$3.96 billion in the quarter ended March 31, immediately said it would appeal, claiming the “unprecedented” amount was unfair.
The company’s lawyer Brad Smith said it would appeal to the EU’s second-highest court, the Court of First Instance.
Microsoft will ask the court if its compliance efforts have been sufficient and claims that the EU had never been clear about what it wanted.
The EU told the company to supply “complete and accurate technical specifications” to developers to help them make software for servers that help computers running Windows, printers and other devices on a network to talk to each other.
It accused Microsoft of using its monopoly position with Windows to elbow into the new server software market.
Ms Kroes said Microsoft’s earlier efforts had not come even close to a readable manual developers could use.
Her decision is based on reports from an independent monitor, computer science professor Neil Barrett, and other technical advisers.
They have had harsh words for Microsoft. In December, Barrett called the documentation “totally unfit” for its intended purpose.
In March, information technology consulting group TAEUS looked again at a revised document Microsoft had supplied. They did not change their tune.
TAEUS described the manual as “entirely inadequate”, “devoted to obsolete functionality” and “self-contradictory”.
It said Microsoft’s documentation was written “primarily to maximise volume while minimising useful information”.
However, Ms Kroes praised the company’s recent work to improve the documentation, saying it was “extremely good”.
On June 20, Professor Barrett had told her that just one out of 70 documents was ready for testing. However, now at least half were in a fit state, he had told her.
It is the first time the EU has fined a company for not obeying an earlier order. Microsoft has three months to pay the fine.