The state of emergency, in force for 30 days, authorises the army to intervene to maintain order and suspends several constitutional rights such as freedom of movement and assembly, according to a decree published in the official gazette.
It covers Lima and the regions of Cusco and Puno, as well as the port of Callao adjacent to the capital.
Supporters of ousted president Pedro Castillo have taken to the streets and blocked roads across the South American country since December, demanding fresh elections and the removal of Boluarte, who has refused to step down.
Protests have been announced for Monday in Lima as well as the marginalised southern Andean regions, which have been the epicenter of the unrest.
Some groups of protesters from the south plan to travel to Lima for a "takeover of the city".
More than 100 protest roadblocks were in place across Peru on Saturday.
The airport in Cusco, gateway to the famed Machu Picchu site, reopened Saturday after being shuttered Thursday, the second time it had been closed due to the protests.
Trains to Machu Picchu were still suspended, and local unions say tourism workers are losing out on up to seven million sols (1.7 million dollars) a day due to the crisis.
The mass anti-government demonstrations first broke out in early December, after Castillo was ousted from office for attempting to dissolve Congress and rule by decree, seeking to prevent an impeachment vote against him.
Peru has been politically unstable in recent years, with 60-year-old Boluarte being the sixth person to hold the presidency in five years.
Castillo, who was being investigated in several fraud cases during his tenure, has been remanded in custody for 18 months, charged with rebellion.
The unrest has been largely concentrated in the southern Andes, where Quechua and Aymara communities live.
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