Steve Ballmer is losing patience. On Saturday, the Microsoft CEO issued an ultimatum to Yahoo’s board of directors, writing a letter that said “now is the time” to negotiate on Microsoft’s bid to buy the company. Ballmer set a three-week deadline for Yahoo’s board to shake hands or else face a proxy fight in which Microsoft would try to oust Yahoo’s directors and nominate its own committee.

A Yahoo spokesperson was not immediately available for comment.

Microsoft (MSFT) has waited nine weeks for Yahoo to accept its offer to buy the company at $31 per share. Yahoo (YHOO) has repeatedly stated that the initial offer of $44.6 billion significantly undervalues the company and rejected the deal in February. Executives from both companies reportedly met earlier this week, but were unable to reach an agreement. In the letter, Ballmer described the “limited interaction” as not “meaningful” and “unfortunate.”

Now Ballmer wants Yahoo to step up the talks. “Our goal in making such a generous offer was to create the basis for a speedy and ultimately friendly transaction. Despite this, the pace of the last two months has been anything but speedy,” he wrote.

Microsoft’s aggressive move suggests that it does not plan to raise its bid and expects Yahoo to accept its offer to acquire the company at a 62% premium. “The public equity markets and overall economic conditions have weakened considerably,” Ballmer wrote in his letter to Yahoo’s board. “At the same time, public indicators suggest that Yahoo!’s search and page view shares have declined. Finally, you have adopted new plans at the company that have made any change of control more costly.”

Microsoft hopes to enter friendly negotiations with Yahoo in the next three weeks. If they fail to reach an agreement, Microsoft will plan a hostile takeover and will authorize a costly proxy fight to try and remove Yahoo’s board. It would then nominate its own slate of directors who would likely approve the deal. Wrote Ballmer, “If we are forced to take an offer directly to your shareholders, that action will have an undesirable impact on the value of your company.”

Ballmer’s letter can be read here.