Under the plan, the Tokyo exchange is looking to buy all of the shares in the Osaka bourse to make it a wholly owned unit but the move has been rejected by the OSE, Kyodo news reported.
This runs counter to current integration talks that have seen the OSE propose that it buy out the TSE before the Tokyo bourse carries out a planned listing of its shares, it said.
Merger talks between the two exchanges started four months ago, but have made little apparent progress due to differences in opinion on how the two sides should proceed.
A spokeswoman for the TSE declined to comment when contacted by AFP, while an OSE spokesman said no details had been confirmed.
The two exchanges first announced plans to start merger talks on March 10, the day before northeastern Japan was struck by a record 9.0 magnitude earthquake and a tsunami.
Discussions so far appear to have been bumpy with OSE President Michio Yoneda calling for an early agreement while TSE President Atsushi Saito has repeatedly said the prior listing of TSE's shares is its priority.
The Tokyo Stock Exchange is the world's third largest in terms of the total value of companies listed, after NYSE Euronext and Nasdaq OMX, according to the Nikkei.
The Osaka exchange serves as the nation's largest market for derivatives trading.
OSE shares were up 8.3 per cent at 391,000 yen by midday.
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