According to British media, England has filed a level 2 charge against Jadeja, who, if found guilty, could be banned for one Test or two ODIs and docked 100 percent of his match fee.
England's retaliation came a day after Anderson was accused of allegedly "abusing and pushing" Jadeja during the first cricket Test at Trent Bridge.
If proved guilty, Anderson will face a ban of two to four Tests or four to eight ODIs.
England captain Alastair Cook said that the counter-charge has been filed against Jadeja.
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"I didn't see the incident to be honest. We had a discussion with (coach) Peter Moores and Jimmy, and we spoke to the hierarchy at the ECB as well. Yes, there has been a counter charge levelled against Jadeja," Cook said.
"Yes I think so. This is tactical from India. This is where all of this has come from. We are surprised it has come to a situation like this to be honest. Level 3 charge is very surprising. It is also possibly because of his competitive streak and it should be about just one incident.
"After hearing Jimmy's version, it is a mountain out of a molehill to be honest," he added.
"It is not something that we have done. Let's realise this fact," Dhoni said.