The Food and Environmental Hygiene Department told Sing Tao that officers seized the meal and inspected the premises after receiving the complaint.
They found hygiene conditions in parts of the shop unsatisfactory and prosecuted the operator under the Food Business Regulation, ordering immediate improvements.
A department spokesman said the investigation covers food preparation, packaging, storage and delivery, according to the South China Morning Post.
He said it would not be appropriate to draw conclusions about when or how the rat entered the food from the online footage alone.
The meal came from Wa Jer Restaurant on the ground floor of Wah Sing Industrial Building on Wah Sing Street, the South China Morning Post reported. The customer paid HK$44 (US$5.60) for a set of satay beef rice noodles, a ham omelet and a drink.
The Standard reported the set normally sells for HK$49 and was discounted 10% for collection, and that she picked it up at about 12:50 p.m.
The woman, who works at a Kwai Chung property agency, told HK01 she usually brings her own lunch and bought takeaway that day only because she was working away from the office.
She said she put the lid straight back on when she saw something moving in the sauce, and that colleagues handled it from there.
An 18-second clip she posted to Threads shows the hairless, pink rat submerged in satay sauce with its limbs still moving.
The Standard reported the footage drew wide attention within hours, with commenters calling the scene terrifying and one joking that the meal came with a free portion of rat sashimi.
Investigation stalls
FEHD said it had invited the complainant to supply further information and give a formal statement but that she had not agreed, HK01 reported, and that it would continue working from the objective evidence already gathered.
Departmental records show the premises holds a valid factory canteen license and that no similar complaint had been lodged against it in the previous 12 months, according to the statement published by Ming Pao.
The owner, identified only as Mike, told Sing Tao Headline he found the incident terrifying and hard to credit, and that he hoped to reach the customer directly to understand what happened.
He said the shop had traded for more than a year without a complaint about rats or insects in a takeaway order.
He questioned how the animal could have survived the kitchen, telling Dot Dot News the beef is cooked fresh and served hot, which he said should have killed a rat rather than left one moving that vigorously.
He would not speculate on whether the incident was a prank, but said he thought it unlikely.
Mike told Sing Tao Headline the premises undergo deep cleaning and disinfection every month, and that the restaurant sits in an industrial district where rats are occasionally seen. He said pest control would be stepped up.
A staff member surnamed Ng told Ming Pao that a professional exterminator visits twice a month and that inspectors had checked the receipts during their visit.
Ng also said the restaurant's closed-circuit cameras were all out of order.
She told HK01 that too many staff handle packaging to establish who assembled the order.
The restaurant closed for the whole of Sept. 8 for a deep clean, HK01 reported, and the department's pest control contractor treated streets around the industrial building that morning.