Formula is popular with mainland Chinese because of concerns about the safety of food processed in China after a series of scandals, notably in 2008 when six babies died from drinking milk tainted with the chemical melamine.
The measures prevent people from taking more than 1.8 kilograms (four pounds) -- or about two cans -- of formula across the border, in a bid to crack down on the so-called "parallel traders" who sell the milk powder for a profit in China.
Offenders face a fine of up to HK$500,000 ($65,000) and up to two years in prison, according to a statement by the customs and excise department.
Tensions between Hong Kongers and mainland Chinese have soared in recent years, fuelled by an influx of mainland visitors blamed for a host of problems, from a shortage of hospital beds to soaring property prices.
The department said customs planned to step up inspection on cargo and baggage of people leaving the territory, coordinating with their counterparts in the mainland.
Eight mainland Chinese and two Hong Kongers carrying a total of 53 cans of formula out of the city were intercepted by customs by Friday afternoon, Assistant Commissioner of Boundary and Ports Yu Koon-hing told reporters.
Reacting to news of the new measures, Crystal Li, a public relations manager and mother of a 5-month-old son told AFP: "I am definitely happy... now that it is available at every pharmacy, it is a lot more convenient."
Li said many pharmacies ran out of formula during last month's Lunar New Year holidays, which typically see an influx of mainland tourists, while accusing some outlets of selling only to parallel traders willing to pay a premium.
"Pharmacies may have a set amount of supplies, but once parallel traders are willing to pay the extra 50 percent, they would rather sell it to them instead of us," she said.
Last month, an online petition to US President Barack Obama to help Hong Kong avoid a baby formula shortage garnered more than 12,500 signatures. It now appears to have been removed from the White House website.
In January Australian supermarkets and pharmacies reported running low on formula reportedly due to Chinese customers trying to secure supplies.