Key Microsoft executives took pay cuts in the last financial year for missing corporate goals, according to the latest regulatory filing by the software giant.

Among those heaviest penalised by Microsoft for the financial year 2011-12, which ended June this year, were chief executive Steve Ballmer and Windows division head Steven Sinofsky.

The two men missed out in collecting the full percentage of bonuses that they were entitled to, according to The New York Times, which in Mr Ballmer's case was 200 per cent of his base annual salary while that of Mr Sinofsky was 150 per cent of his yearly take home.

In the document filed before the U.S. Securities and Exchange Commission (SEC), Mr Ballmer was shown to have only received 91 per cent of his CEO pay, which Microsoft was at around $US685,000.

His bonus for spearheading Microsoft's global business operation as of June 2012 was $US620,000.

As for Mr Sinofsky, the man chiefly responsible for Microsoft's core product - Windows, he only pocketed $US7.65 million for the same period, or only about 90 per cent of what he should have received.

Besides taking on the high-profile role of fronting for Microsoft, the two men also carry with them the biggest burden of realising the company's growth targets and in the last financial cycle, such thrust apparently fell short of expectations.

Windows saw a revenue decline of three per cent in the period while its mobile phone version only achieved what the Microsoft regulatory filing described as "modest growth."

The company's online business appeared to have stagnated too in the last financial year due to "slower than planned progress," under the baton of Mr Ballmer.

The two Microsoft officials also took the fall for the firm's regulatory problems in the European market, the SEC filing said.

Mr Sinofsky's Windows division failed "to provide a browser choice screen on certain Windows PCs in Europe as required by its 2009 commitment with the European Commission," the Microsoft document was reported by Reuters as saying on Tuesday.

The pay cuts easily rendered Mr Ballmer as the lowest paid executive in Microsoft's hierarchy for the financial year concerned, with his rate as CEO already one of the lowest by U.S. standard, Reuters noted.

But his compensation scheme was actually of Mr Ballmer's own design, The NY Times said, pointing too on an arrangement in which the CEO was allowed by Microsoft's board to own some 333 million shares of the software giant.

Present value of those holdings, the U.S. publication added, is at around $US10 billion, putting Mr Ballmer almost in the same league of his predecessor, Microsoft co-founder Bill Gates.

Since taking over from Mr Gates 12 years ago, Mr Ballmer has encountered serious challenges in plotting the growth strategy of Microsoft, his biggest mistake, according to analysts, was overlooking the rise of mobile computing the past half-decade.

That oversight led to Microsoft's steady decline while its archrival, Apple - a firm that it routinely beats during much of the late 1980s through the 1990s, flourished with innovative devices.

By early 2012, Mr Ballmer and Microsoft witnessed Apple's inevitable ascent as the world's most valuable company, a distinction that Microsoft once held many years ago.