The zip codes -- 11205 in Clinton Hill, 11206 in Bushwick and 11211 and 11249 in Williamsburg -- are all in predominantly Orthodox Jewish communities.
"Since the Emergency Order took effect, the Health Department carefully investigated cases with the help of its disease detectives," the health department said in a press release. "Many of the people who were contacts of individuals with measles had proof of vaccination, however the Health Department identified three children who were exposed to the measles but still unvaccinated as of April 12."
In addition to the three people fined for being unvaccinated, the city also closed four additional schools for failure to provide vaccination and attendance records, the city said.
The health department had ordered United Talmudical Academy, a yeshiva preschool, closed on Tuesday, but it has now been allowed to reopen.
As of Thursday, there had been 359 measles cases in Queens and Brooklyn since the beginning of the outbreak last October, including 74 since the emergency order was issued on April 9.
"The initial child with measles was unvaccinated and acquired measles on a visit to Israel, where a large outbreak of the disease is occurring," according to the health department. "Since then, there have been additional people from Brooklyn and Queens who were unvaccinated and acquired measles while in Israel."
A lawsuit filed by five unnamed parents asking for the emergency order -- and mandatory vaccinations -- to be vacated "as arbitrary and capricious and contrary to law" was also shot down on Thursday.
"The pivotal question posed for this court's determination is whether Respondent Commissioner has a rational, non-pretextual basis for declaring a public health emergency and issuing the attendant orders challenged herein," Kings County Judge Lawrence Knipel wrote in his decision.
The judge found the emergency declaration to be well-founded, and followed up, writing, "A fireman need not obtain the informed consent of the owner before extinguishing a house fire. Vaccination is known to extinguish the fire of contagion."
Measles can cause fever, runny nose, diarrhea and pneumonia. Severe cases can even result in death, especially in infants, children and people with compromised immune systems.
The vaccine is considered "very safe" and effective by the Centers for Disease Control and Prevention (CDC), which also debunks any concerns -- often held by so-called anti-vaxxers -- that the vaccine could cause autism.
"Vaccine safety experts, including experts at CDC and the American Academy of Pediatrics (AAP), agree that MMR vaccine is not responsible for increases in the number of children with autism," the CDC states on its website.