Officials deployed dozens of shuttle buses, along with army lorries, to ferry stranded medical personnel and workers of authorised businesses.
Most domestic flights to and from the capital were cancelled, and night curfews will return in places.
Crowds had gone to some supermarkets on Monday to stock up on food after the hasty return to a lockdown sparked panic-buying.
The lockdown is milder than was first one imposed, which largely confined most people to their homes for months, but is more severe than the quarantine restrictions the capital had been under recently.
It is being imposed in metropolitan Manila and outlying provinces for two weeks.
Businesses previously allowed to partly reopen, including barbershops, gyms, dine-in restaurants and tourist destinations, will again be closed.
Authorised companies including banks, health and food processing firms must shuttle their employees between home and work.
Travelling by bike, motorcycle and private car is allowed for essential reasons, but mass transit will be closed.
President Rodrigo Duterte agreed to reinstate the lockdown after medical groups warned the health care system was being overwhelmed by Covid-19 patients.
Health officials reported a record-high daily tally of 6,352 new infections on Tuesday, bringing the country’s total to more than 112,500, including 2,115 deaths.
