The Ministry asked AAP to furnish details of overseas fundings after suspecting that it might have violated FCRA provisions.
The party termed the Centre's move as "political witch hunt".
"It is a clear case of political witch hunt. All the agencies at the Centre's disposal have been unleashed against Aam Aadmi Party, its government in Delhi and its ministers. Which is very dangerous for democracy," PTI quoted AAP as saying in a statement.
"It is worth mentioning that the Ministry of Home Affairs had given us a clean chit before the high court on this issue and now they are sending us fresh notices," it said.
AAP leader and its spokesperson Raghav Chadha alleged that the Centre has unleashed all the agencies against AAP.
"CBI raided yesterday and foreign funding investigation today, Centre's vendetta comes out as an all out war on this political toddler called AAP. All agencies at Centre's disposal have been unleashed against AAP, its Govt in Delhi and its ministers. Very very dangerous for democracy," he said.
"Wondering what happens when a political infant like AAP chooses honest, transparent politics? Frivolous allegations and investigation. Political titans witch-hunting AAP must realize our collective morale is strong enough to weather your baseless, short lived investigations," he tweeted.
PTI quoted an MHA official as saying the notice to AAP was part of its "routine" queries sent to a few other political parties regarding overseas funding to them.
The official reportedly stressed that it was not a show cause notice and a decision would be taken on any further inquiry only after the AAP submits its reply.