JYP Entertainment represents 16-year-old Taiwanese pop star Chou Tzuyu, who recently made a video apologising for waving a Taiwanese flag on S Korean TV.
The company denied coercing her into saying sorry to appease angered Chinese audiences, a key market for JYP.
The row erupted on the eve of Taiwan's election, which was won by pro-independence Tsai Ing-wen.
Taiwan has been ruled separately since the end of the Chinese civil war in 1949, but it is seen by China, as a breakaway province which it has  threatened to take back by force if necessary.
JYP told South Korea's Yonhap news agency that its website had been inaccessible since Saturday, the day after Chou's apology was put online.
It said it suspected a DDoS (distributed denial of service) attack, where multiple users visit a website repeatedly to overwhelm its servers, but that it did not know where it was coming from.
It said getting the site back on line "may take a while".
Chou, a member of the Kpop group Twice, carried the flag of the Republic of China - Taiwan's official name - in a section on a South Korean TV show in November introducing the band members.
The scene didn't appear on air but was widely shared online in China, and brought up in Taiwan during the election campaign by a noted anti-independence celebrity.
Chou was widely criticised and the band had an New Year's Eve appearance on Chinese TV cancelled.
Last week, JYP published a video online of Chou meekly apologising for having appeared to back Taiwanese independence.
"There's only one China. The two sides of the Taiwan Strait are one. I will always consider myself as a Chinese person and feel proud of this.
The BBC's Cindy Sui in Taipei say that many people in Taiwan saw Chou's apology as humiliating for her and Taiwan.
To many, she says, it was a reminder of their biggest peeve - that Taiwan, which they consider a sovereign country, is not recognised as one officially and is denied membership in the United Nations as well as in many international groups.
Meanwhile, a South Korean multicultural group has said it is lodging a formal complaint with the national rights watchdog about Chou's treatment.
The Center for Multicultural Korea (CMCK) said it would ask the commission to "investigate whether the apology was forced or not".
A South Korean company at the centre of a row about a flag waving pop star says its website has been hacked.