The software giant is already facing €777.5 million in EU fines over anticompetitive practices, and faces penalties of up to €3m a day for what the European Commission says is its continuing failure to comply with a previous order.
"Microsoft is constantly gaining market share and that is what is worrying me in the work group server market," said Kroes, referring to the kinds of servers which help individual computers connect to one another and to printers in offices.
Addressing Microsoft, she said: "As a consequence of your abusive behaviour you are getting positive results for the company – that's not acceptable".
Kroes is concerned that Microsoft's already dominant share of the workgroup server market in the late 1990s has grown even further. Her office said that it had between 35% and 40% of the market in 1999, but now controls 75% of that market.
In 2004 the EU fined Microsoft €497m in its antitrust case against the company. It was given a deadline to comply with the ruling. In July last year the EU fined it a further €280.5m for failing to comply with the ruling by the deadline. It is also threatening continuing fines of up to €3m a day.
Kroes's office claims that Microsoft gains an unfair advantage in the workgroup market because computers running the Windows operating system, which has a near-monopoly in offices, work more smoothly with servers running Microsoft software.
It says that the reason for this is that Microsoft will not release software source code which would allow third party server makers to ensure that their machines and software worked as smoothly with Windows-operated machines.
Microsoft says that its source code software is valuable intellectual property and has now offered to make it available, though at a price. The European Commission says that the price is too high.
Microsoft is opposing the original 2004 ruling against it, and a court decision on that ruling is expected later this year.