President Vaira Vike-Freiberga received the Japanese couple at Riga Castle in the old town of the capital, before laying flowers at the Freedom Monument in the city center.
Hundreds of people flocked around the monument square on a warm sunny day, waiting to catch a glimpse of the imperial couple.
Later, Akihito and Michiko were to visit the Occupation Museum, which exhibits life in the former Soviet republic that was occupied after Stalin's Red Army invaded the Baltic states in 1940.
Latvia, a nation of 2.3 million, like its neighbors Estonia and Lithuania, split from Moscow in 1991 after 50 years of occupation.
The imperial couple were also to view an exhibit of fossilized fish specimens, specially organized for Akihito, whose lifelong passion has been marine biology.
On Thursday, Japanese Ambassador Seiichiro Otsuka and Latvian Foreign Minister Artis Pabriks planted sakura trees in a central Riga park in honor of the visit.
The imperial couple arrived in Riga from the Estonian capital, Tallinn, where they met President Toomas Hendrik Ilves and other leaders. They were scheduled to visit Lithuania on Saturday, before flying to London on Sunday, the last leg of their journey.
Earlier this week, they met Sweden's King Carl XVI Gustaf and Queen Silvia in Stockholm. They also took part in the 300th anniversary celebrations for the birth of the 18th-century Swedish scientist Carl Linnaeus, who developed the modern system of classifying plants and animals.