Japan has confirmed it wanted fugitive Sea Shepherd leader Paul Watson to be held for questioning before he broke bail in Frankfurt and fled Germany.

The chief cabinet secretary, Osamu Fujimura, said the government was still attempting to determine facts around the flight of Watson, who led his group in eight campaigns against the Japanese whaling fleet in the Antarctic.

Fujimura told reporters in a Tokyo press conference that Japan had been in the early stages of an official approach to Germany over the case of  Watson.

"The Japanese government has tentatively submitted a request to incarcerate the individual for further investigation by the Japanese government,"  Fujimura said through an official interpreter.

Watson had been detained on €250,000 bail in Germany for 70 days while Costa Rica sought his extradition over an alleged navigation offence that was revived after a decade.

Japanese officials repeatedly described Watson as an eco-terrorist in the escalating Antarctic conflict.

This summer he planned to use a four-ship fleet to shut down the "scientific whaling" operation.

In 2010 Japan sought his inclusion on Interpol's blue notice list, which requested his whereabouts be noted, but did not ask for his arrest.

Watson said before his arrest in Germany that he believed the notice had lapsed.

Following his departure from Germany, for an unknown destination, a Frankfurt court issued a new arrest warrant.

Japan has repeatedly asked Australia to act against Watson and Sea Shepherd, but a series of Australian Federal Police investigations have not resulted in any charge.

- Sydney Morning Herald