Statistics on the website of the Special Committee For Ensuring Access to Covid-19 Vaccine Supply (JKJAV) show that the two are the first among the country's 13 states and three federal territories to reach 100% registration among their respective target populations aged 18 and above.
As at 11.59pm on Sunday (June 20), a total of 1,385,741 people in Kuala Lumpur have registered for the vaccines, while in Putrajaya the figure was 76,536.
Selangor, with 3,745,931 registrations (78.90%), is in third place.
Sabah, meanwhile, has the lowest percentage of registrations at 29.18% or 804,851.
In terms of total vaccinations, Kuala Lumpur and Putrajaya were also in the top two among the states and federal territories.
As at 11.59pm on June 20, 724,684 or 53.74% of Kuala Lumpur's population aged above 18 had received the first dose of vaccine.
Of the total, 141,094 have received their second jabs and as such have been fully vaccinated.
In Putrajaya, 33,272 or 49.15% of its population have gotten their first shot, and from that figure 20,073 have received their second dose as well.
In Selangor, the percentage of people who have received their first dose was relatively lower, at 13.53% (642,249).
According to a post on JKJAV's Facebook page, a total of 4,202,601 people or 12.9% of Malaysia's population have been given their first dose so far.