Chinese paper 21st Century Business Herald cited a former staff, identified by a pseudonym, as saying Eli Lilly paid out 30 million yuan ($4.9 million).
The claims come at a time when China is investigating some drugs firms over similar bribery allegations.
Eli Lilly said it had launched an internal probe last year after a former manager made similar allegations against it.
“At the time of the allegations, we did an exhaustive investigation to search for any evidence of kickbacks,” the company said in a statement.
“Although we have not been able to verify these allegations, we take them seriously and we are continuing our investigation.”
The drugmaker said it interviewed employees, monitored emails and audited expense reports as part of its internal probe.
However, it said it had not employed any sales managers by the name of Wang Wei, who was mentioned in the 21st Century Business Herald report.
Eli Lilly is the latest foreign drugmaker to be engulfed by such claims in China.
Earlier this week, a British risk consultant, Peter Humphrey, was formally arrested by Chinese authorities amid a continuing probe into pharmaceutical companies.
One of the companies being probed, GlaxoSmithKline (GSK), is reportedly a former client of Peter Humphrey’s firm, ChinaWhys.
Chinese authorities have accused GSK of directing up to $500 million through travel agencies to facilitate bribes to doctors and officials.
GSK has said that some senior executives in its China office appeared to have broken the law and several GSK employees have also been detained over the last few weeks.
In July, Chinese police had visited the Shanghai office of AstraZeneca and took an employee in for questioning.
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