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Investigations have revealed that a Tampa socialite -- Jill Kelly -- sent 'flirtatious emails' to John Allen, the commander of US forces in Afghanistan.
General Allen was put under investigation after Federal Bureau of Investigation agents, probing email threats sent by Petraeus's mistress, stumbled upon messages the US commander sent to another married woman.
United States President Barack Obama has put on hold the nomination of Allen as the next commander of the US European Command.
US Defence Secretary Leon Panetta, in a statement, said the FBI has referred to him the matter involving General John Allen.
The ripples in the US military came as Panetta demoted a former head of the Africa command on charges of lavish travel and spending.
General William Ward, former commander of US Africa Command, would now be retired at the grade of lieutenant general, Pentagon Press Secretary George Little said.
Hours after reports of Allen's involvement in the infamous Patraeus affair came to light, the defence secretary cautioned against reaching early conclusions about the veracity of allegations against the top US commander in Afghanistan.
"No one should leap to any conclusions here," Panetta told reporters in Perth.
He said the 59-year-old general has "my continued confidence to lead our forces in Afghanistan".
The four-star general also received the backing of his Commander-in-Chief
President Barack Obama.
According to Pentagon officials, the married general denies any sexual liaison with 37-year-old Kelly, but the sheer volume of correspondence between him and the socialite continues to be unearthed by the FBI agents.
Allen was scheduled to face a Congressional hearing to confirm his promotion to the post of North Atlantic Treaty Organisation's supreme commander in Europe, but will now have to remain in Kabul till the probe is over.