The future of both organisations was said to be in question because of financial and operational pressures. The Royal Opera House has been plagued with problems in its pounds 214m refurbishment.
Launching the inquiry, Chris Smith, the Heritage Secretary said that with pounds 78m of lottery money involved he wanted to be sure the scheme was carried out "with probity".
The news came after Arts Council secretary general Mary Allen's appointment last month as chief executive of the Royal Opera House. She replaced Genista McIntosh, who resigned only 18 weeks into the job, apparently through ill health.
Arts Council chiefs were unhappy Ms McIntosh was replaced without the post being advertised. They asked Ms Allento leave her Arts Council job immediately to avoid any implication of a clash in responsi- bilities.
The ROH is an independent body, but because of its level of public funding the Arts Council has an interest in the way it is run.
Lord Gowrie, who stands with the former camp, has publicly described the ROH's plans for the Royal Opera and the Royal Ballet during redevelopment as "a shambles".
Meanwhile Dennis Marks, the ENO's general director, revealed that he had submitted his resignation in March, after being asked to implement cost-cutting to reduce the ENO's pounds 4m deficit.
The ENO is said to be in financial trouble, despite an pounds 11.9m Arts Council grant, and has applied for pounds 3m of emergency lottery money from the Arts Council.
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