The New York Times said incoming President Park Geun-hye has been warning Lee not to abuse his presidential power by pardoning criminals, but Lee said Tuesday he is still the president.
Lee said the 13,000 people pardoned under his rule are far fewer than those pardoned by his predecessors.
The Times said every South Korean president has granted amnesty more than once a year by freeing criminals or restoring the full rights of ex-convicts, and the decisions often affected thousands of people at a time.
The Times said it is customary for presidents to hand down pardons near the end of their terms, and Lee approved pardons Tuesday for 55 people, including two friends who were convicted of bribery and have served less than half of their sentences.
As a result, Park's team is criticizing Lee.
"Pushing ahead with pardoning those involved in irregularities and corruption will receive a national reproach," Park spokesman Yoon Chang-jung said Tuesday after the presidential pardons were announced. "President Lee should bear all responsibility."