The fund manager, who made his name warning about Lehman Brothers Holdings Inc's
Einhorn's comments, which echo what some investors have said for some years in private, caused a stir on Wall Street and helped Microsoft shares climb 2 percent on Thursday to $24.67.
His continued presence is the biggest overhang on Microsoft's stock, Einhorn told fellow fund managers at the annual Ira Sohn Investment Research Conference in New York.
Microsoft's nine-person board, including Chairman and co-founder Bill Gates, supports Ballmer, a source close to the board told Reuters on Thursday. Microsoft itself declined comment.
Gates, who co-founded the software company in 1975 and is still the largest shareholder with 6.6 percent of the company's stock, is generally regarded as the one person who could make the decision to switch management.
Bill Gates is a ruthless capitalist. If he wanted to, he'd walk Ballmer to the door himself, said a fund manager at one of Microsoft's largest shareholders, who asked to remain anonymous.
Gates, who spends most of his time on his philanthropic foundation, has given no indication he is considering a change. A representative declined comment on Thursday.
Other investors acknowledged Microsoft's stock has suffered under Ballmer, but stopped short of calling for his ouster.
I thought the board was firmly behind Steve, and the only way Steve was going to leave was if Steve wanted to leave, said Eric Jackson at hedge fund Ironfire Capital, which sold its position in Microsoft last autumn, disappointed the company would not lift its dividend higher.
I don't see anybody else on the management team at Microsoft that I think would be much better than Ballmer.
Whitney Tilson, founder and managing partner of T2 Partners LLC, which holds Microsoft stock, suggested Ballmer might be running out of steam.
This dissatisfaction with Ballmer, with the company, is more than baked into the stock, said Tilson in an appearance on financial news channel CNBC. When you've been the top dog so long, how do you become hungry again?
APPLE ROARS PAST
Microsoft -- the largest U.S. company by market value in the late 1990s -- has been overtaken by Apple Inc
Before Thursday's gain, the stock had been down 6 percent in the past two weeks after Microsoft agreed to pay $8.5 billion for Internet phone service Skype, a move that mystified many investors.
Einhorn said it was time for Microsoft to consider strategic alternatives for its money-losing online business, which has so far failed to win share from Google Inc
Clearly, some people are calling for a change, said Sid Parakh, analyst with McAdams Wright Ragen. If you look at the financial performance, that's been fine. But I think the issue is broader than that.
If you look at search, mobile, tablet, these are areas they should have been investing in, and they have -- but they weren't able to get it right, he added. But: If there was any reason to believe the board was not with Steve, it would be a different situation. But the board seems to be behind Steve.
The online services unit, which runs the Bing search engine and MSN Web portal, had a loss of $726 million last quarter and has now lost $7 billion in four years.
What it boils down to is that Microsoft has had a load of initiatives which haven't shown traction yet, said one U.S. equity fund manager at an investment house featuring on the list of Microsoft's top 40 largest shareholders. The most recent one is to buy Skype, and the perception on that is that it is overvalued. We won't know what revenue synergies are until two, three years down the road.
Microsoft created the platform on which Google and the Internet can go forward, and it's not exactly yesterday's technology; but they do have to connect more with the mobile computing world and they haven't really done that.
BGC Partners Colin Gillis credited the rise in Microsoft's stock price Thursday to fast money, or investors looking to take advantage of an undervalued stock.
It's on. David Einhorn likes to shake things up, Gillis said. As for Microsoft's stock staying flat over a decade, the question is, is it because of Ballmer, or is it because people are concerned about a post-PC era?
(Additional reporting by Sinead Cruise in London, Sinead Carew and Paul Thomasch in New York, writing by Edwin Chan; editing by Gerald E. McCormick, Dave Zimmerman and Andre Grenon)