Chile's first elected right-wing president in 52 years won office promising to improve the economy. Now, he says he will be the "reconstruction president".
He also advised residents to "dry [their] tears and put our hands to work".
But relief efforts stalled on Thursday as more than 10 earthquakes shook Chile in a span of six hours.
The navy issued a tsunami alert along the coast. Sirens sounded in Constitucion, one of the strongest-hit cities in the February 27 quake and police ordered people away from beaches.
The freshly inaugurated president said there was "significant damage" in Rancagua, a city almost 100 km south of the capital.
The strongest at 6.9, the aftershock nearly matched the 7.0 magnitude quake that devastated Haiti on January 12.
The inauguration had lasted just 30 minutes, marked by three of the aftershocks. Pinera then travelled to Constitucion to inspect the damage caused by the earthquake last month.
He then travelled back to the capital and detailed his visit, saying that "lots of people are still missing and I saw people in anguish today, as well as people with hope, who asked us not to abandon the search for those still missing."
"Thousands and thousands were victims of this earthquake and tsunami, lots because they were injured and some because their suffered huge losses," Pinera said.
"Without any doubt the human cost of this tragedy and the fact many are still missing, are the most painful and sensitive part of this tragedy."
'State of catastrophe'
Lucia Newman, Al Jazeera's correspondent in Vina Del Mar, where the president attended a presidential luncheon, said Pinera declared a state of catastrophe in what is called the zona libertador, because of the damage caused in Rancagua.
"He was ordering troops there to ensure there would be no looting, that there would be security there, no repetition of the sort of scenes that we saw in the city of Concepcion following the original earthquake," Newman said.
The handover of power from Michelle Bachelet, a popular centre-leftist, was celebrated with an austere midday ceremony, toned down out of respect for those still mourning the dead.
Officials have identified 497 dead from the February 27 quake and tsunami, after revising down an earlier death toll of 802, which mistakenly included lists of the missing.
Pinera's election marks a shift to the right in Latin America where a generation of centre-left and socialist leaders are in power.
Fellow conservative presidents Alan Garcia of Peru and Alvaro Uribe of Colombia attended the inauguration along with leftist leaders such as Argentine President Cristina Fernandez and Bolivia's Evo Morales.