"We are distressed by the unseemly controversy that has arisen about some unauthorised tweets from our twitter accounts," Tharoor said in a joint statement which has appeared on a Facebook page.
The controversy started after intimate messages, allegedly sent to him by a Pakistani woman journalist, were posted on his widely-followed twitter account.
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Tharoor's wife Sunanda claimed on the micro-blogging site that she had posted from her husband's account, the allegedly private messages sent to him by Lahore-based journalist Mehr Tarar, to show the world "how she is stalking my husband".
"We wish to stress that we are happily married and intend to remain that way. Sunanda has been ill and hospitalised this week and is seeking rest. We would be grateful if the media respects our privacy," the statement said.
It further added that "distorted" versions of comments allegedly made by his wife Sunanda had appeared in the media.
"Various distorted accounts of comments allegedly made by Sunanda have appeared in the press. It appears that some personal and private comments responding to these unauthorised tweets - comments that were not intended for publication - have been misrepresented and led to some erroneous conclusions," the statement added.
The twitter handle of Tharoor, one of the most popular Indian politicians on the micro-blogging site, was allegedly hacked yesterday.
The tweets instantly created a buzz on social media websites.
"Sorry folks, my @Twitter account has been hacked and will be temporarily deactivated. Bear with me while we solve this," his twitter page had read.