The actress, who was recently named in a New York Times expose alleging sexual misconduct by Hollywood mogul Harvey Weinstein, has been tweeting about the scandal since it broke.
Weinstein was forced out of his company after several women came forward alleging he had harassed them and acted inappropriately. More accusations, including alleged rape, have since surfaced.
McGowan Instagrammed a photo of a notification from Twitter late Wednesday saying the site had "determined that this account had violated the Twitter Rules, so we temporarily limited some of your account features."
This left McGowan unable to tweet for 12 hours, according to the notification. The caption on her official Instagram account said: "TWITTER HAS SUSPENDED ME. THERE ARE POWERFUL FORCES AT WORK. BE MY VOICE."
The company has since tweeted an explanation.
"We have been in touch with Ms. McGowan's team," Twitter said in a tweet on Thursday. "We want to explain that her account was temporarily locked because one of her Tweets included a private phone number, which violates of our Terms of Service."
Twitter clarified that McGowan's account had been unlocked and the offending tweet was removed.
"Twitter is proud to empower and support the voices on our platform, especially those that speak truth to power," the final tweet said. "We stand with the brave women and men who use Twitter to share their stories, and will work hard every day to improve our processes to protect those voices."
Twitter does not typically comment on individual accounts for privacy and security reasons. Twitter can temporarily block a user for a variety of reasons, including abusive content and threats.
But speculation on why her account was suspended became the center of online chatter.
"We will be clearer about these policies and decisions in the future," Twitter said in a tweet.
Some of McGowan's tweets alleged that people in the industry, including Weinstein's brother Bob and actor Ben Affleck, were aware of what's been called Hollywood's open secret.
The Weinstein Company's board of directors -- which includes Bob Weinstein -- issued a statement Tuesday stating "these alleged actions are antithetical to human decency."
"These allegations come as an utter surprise to the Board," the statement said. "Any suggestion that the Board had knowledge of this conduct is false."
Affleck later posted a message on social media about Harvey Weinstein, who helped launch his career with the 1997 film "Good Will Hunting."
"I am saddened and angry that a man who I worked with used his position of power to intimidate, sexually harass and manipulate many women over decades," Affleck wrote. "The additional allegations of assault that I read this morning made me sick."
McGowan called for the board of Weinstein's company to be dissolved in a tweet. She believes it was complicit in Weinstein's alleged behavior.
"If you believe The Weinstein Company should completely dissolve after 30 years of sexual abuse against innocent women please join me in signing this petition to honor the victims and their bravery," the petition reads.
As of Thursday morning, it had more than 13,000 signatures, exceeding its goal of 10,000.
The "Charmed" star was not quoted in the Times story. CNN has not spoken with McGowan about the alleged sexual misconduct.
Film director Paul Feig, who has condemned Weinstein, tweeted about the move to block McGowan's Twitter account.
"Wow, @Twitter, seriously," Feig wrote. "THIS is the account you suspend but not Trump who threatened to wipe out another country? Suspend me too, please."