In a statement posted on the Hong Kong stock exchange on Friday, Cathay said Hogg had resigned "to take responsibility as a leader of the Company in view of recent events".
He has been replaced by Augustus Tang, a veteran of the Swire Group conglomerate, Cathay's main shareholder.
Another senior Cathay executive, Chief Customer and Commercial Officer Paul Loo, also announced his departure and gave the same reason in the statement.
Cathay has had a torrid week after it became ensnared in a hardening of rhetoric from Beijing over ten weeks of anti-government protests that have rocked Hong Kong.
Over the last two weeks the airline emerged as a target on the mainland after some of its 27,000-strong workforce took part in, or voiced support for, the protests.
Chinese state media wrote a series of condemnations of Cathay, accusing it of not doing enough to rein it its workers.
Then China's aviation regulator demanded that the airline prevent such staff from working on flights to the mainland or those routed through Chinese airspace.
Cathay swiftly moved into damage limitation mode, firing four members of staff associated with the protests -- including two pilots -- agreeing to comply with the new regulations and releasing a series of statements supporting Hong Kong's embattled government.
But is appears none of these moves were enough to save Hogg, who has been credited with helping to turn the airline profitable after two years of losses.
"The Board of Directors believes that it is the right time for new leadership to take Cathay Pacific forward," Cathay said in a statement.
In the same statement Hogg was quoted as saying: "These have been challenging weeks for the airline and it is right that Paul and I take responsibility as leaders of the company."
Hogg has been replaced by Augustus Tang, a veteran of the Swire Group conglomerate, Cathay's main shareholder.