Atsushi Yamagami was given 21 months and ordered to pay more than $18,000 in fines after pleading guilty in August to one felony count of smuggling. He could have faced a maximum of 20 years in prison.
In a letter to U.S. District Judge George King, Yamagami apologized and promised never to engage in animal smuggling again.
"I am extremely ashamed and remorseful about my actions," he wrote.
Yamagami, 39, and Norihide Ushirozako, both of Osaka, were arrested in January 2011 at Los Angeles International Airport as part of an undercover investigation by federal agents known as Operation Flying Turtle.
The 55 turtles and tortoises were hidden in snack food boxes found in a suitcase. Federal prosecutors argued the measures taken by the men constituted animal cruelty and the reptiles posed a risk of transmitting salmonella.
The animals are protected by an international endangered species agreement and can only be imported with a permit.
After the animals were smuggled into the U.S., Yamagami sold or traded them at pet shows and used the proceeds to purchase snakes, turtles and tortoises native to North America, which were then smuggled to Japan for resale, authorities said.
Yamagami paid couriers to hide wildlife inside luggage, according to court documents. Authorities believe Yamagami and his couriers took more than 40 trips to and from the U.S. between 2004 and 2011.
Ushirozako also pleaded guilty in August to a smuggling charge and was released from federal custody after being sentenced to time served, which totaled about seven months.