Marissa Mayer breaks her silence on Yahoo’s telecommuting policy

Marissa Mayer at the Great Place to Work conference

FORTUNE — In the closing keynote at the Great Place to Work conference at the Hyatt Regency Century City in Los Angeles Thursday, Yahoo CEO Marissa Mayer defended her decision to kill the company’s popular work-from-home policy.

Until now, she had refused to comment on the switch, previously saying via a spokesperson that the company does not discuss internal matters. The come-to-work order was first reported when a leaked memo from Yahoo’s human resources director was published by a tech blog in February.

Addressing a crowd of human resources professionals, Mayer launched into a speech about the Internet giant’s “already vibrant” culture, but after a few minutes interrupted herself and announced, “I need to talk about the elephant in the room.” Immediately an image of a purple elephant, with large while letters “WFH” (work from home) painted on its side, appeared on projection screens in the hotel auditorium.

She repeated a key phrase the company used in a statement it released after the memo was leaked: “It’s not what’s right for Yahoo right now,” and added “It was wrongly perceived as an industry narrative.”

Her remarks were a response, two months later, to the many critics who lambasted the policy reversal by calling it a step backward for workplace flexibility. Flex options are the norm at big tech companies, which have inspired many other industries to adopt similar programs. One week after the Yahoo (YHOO) announcement, Best Buy (BBY) said it would end its flexible work policy as well.

MORE: Tony Hseih: Working from home alone is the real culprit

Mayer defended her decision by first acknowledging that “people are more productive when they’re alone,” and then stressed “but they’re more collaborative and innovative when they’re together. Some of the best ideas come from pulling two different ideas together.” The shift in policy affects roughly 200 of Yahoo’s 12,000 employees.

As an example of that collaboration, Mayer touted the newly-launched Yahoo Weather app for iOS, which uses built-in geolocation technology in Flickr photo albums to help users get a more accurate image of local weather — an idea, she explained, originated by two software engineers who work in the same office.

By using the image of a purple elephant in her presentation, Mayer poked fun at her own management gaffe, which, as Fortune’s Pattie Sellers argued, wasn’t the policy itself but how it was unveiled to the public. Why she refused to speak publicly about it until now is anyone’s guess, but waiting so long to address the matter only attracted more attention. She couldn’t have earnestly spoken before a group of HR specialists without explaining the policy shift.

Before joining Yahoo, Mayer helped create the highly-lauded culture at Google, which currently holds the No. 1 spot on Fortune’s list of the 100 Best Companies to Work For. Already it seems she’s on track to replicate some of Google’s workplace innovation.

In the first nine months of her Yahoo tenure, Mayer threw out the company’s overly complicated 22-page travel and expense policy and ordered a revamped version “that humans could understand.” She also distributed smartphones to the staff and offered free food at the office — both staples at Google (GOOG).

Challenged with turning around the troubled Internet company, Mayer has made resetting the culture at Yahoo a top priority. “My goal is not to change the culture, but to amplify its greatness,” she told attendees. Yahoo previously has appeared on Fortune’s 100 Best Companies list three times, most recently in 2008.

The invitation for Mayer to speak at yesterday’s conference was extended last fall, long before the telecommuting controversy made headlines. Conference host Great Place To Work, a consulting institute that specializes in employee satisfaction, is Fortune’s research partner for the 100 Best Companies list.

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