The governor had addressed the audience at the Forum for Integrated National Security, backed by the RSS, Sunday.
There was palpable tension after Wanchoo repeated United Progressive Alliance chairperson Sonia Gandhi's reference to "poisonous seeds" while speaking at the function about "reactionary forces".
The Nationalist Congress Party (NCP) claimed that the Bharatiya Janata Party (BJP) government in Goa was trying to start "hardcore" RSS operations in the state through the back door.
"The governor's presence at the Sangh-backed event was to expose these saffron designs. His speech at the RSS-backed FINS and his reference to 'poisonous seeds' in the presence of Indresh Kumar makes that clear," NCP vice president Trajano D'Mello told a press conference at the party's state headquarters in Panaji.
In his speech on Sunday, Wanchoo did not take names but said, in the presence of senior Sangh leaders like Indresh Kumar as well as top state RSS leaders, that "reactionary tendencies and forces are at work to thwart our progress and to sow poisonous seeds of terror among the peace-loving citizens of our country".
The analogy used in the speech was near-identical to the one used by Congress president Sonia Gandhi to attack the BJP at a rally on Saturday.
The governor also slighted a speaker, a lieutenant general, for repeatedly blaming systemic ills on "political will".
"It has become the fashion to speak about lack of political will," Wanchoo said extempore, deviating from his written speech.
The function was organised by FINS as part of a two-day seminar on the subject of coastal security at a resort in the beach village of Calangute, 15 km from the state capital.
Indresh Kumar, a national executive member of the RSS, is the chief patron of FINS, which is looking to set up a centre for academic studies in Goa.
"Indresh Kumar has been chargesheeted by the Rajasthan police in the Ajmer blast case for promoting Hindu terror. What was he doing in Goa promoting a security organisation?" D'Mello said.
The NCP also criticised Goa Chief Minister Manohar Parrikar for granting FINS the chance to operate the proposed academy for defence studies which the Goa government is in the process of setting up.
"The NCP wants the chief minister not to venture with such tactics of indoctrinating RSS ideology by bringing in academies in the form of defence study, which is backed, controlled and financed by fanatics," D'Mello said.
The NCP also criticized the Goa government's decision to convene a five-day budget session of the state legislative assembly on days which coincide with the annual carnival in the state that begins Feb 28 and stretches till March 4.
The five-day session of the Goa assembly is expected to start March 3.