He also said that "divisive forces" were giving communal colour to the incident.
Returning to Indore, his hometown, after being elected as the VHP international president, Kokje told reporters at the airport, "Such incidents are shameful in a country which has been a big centre of 'samskara'. We condemn this incident. The rape is against human rights.
"The way we say there is no religion of terrorists, in the same way, why the religion of the victim and accused should be seen in the cases of rape?" he asked.
"The people who are talking in the communal way about the Kathua incident are the divisive forces in the society, these people should be strongly condemned," Kokje said.
To a question, he said the VHP was not in favour of making any changes to the Scheduled Castes and Scheduled Tribes (Prevention of Atrocities) Act, and its provisions should not be weakened.
Kokje, a former judge of the High Courts of Madhya Pradesh and Rajasthan, added, "Innocent people should not be persecuted, but the guilty should not be spared either."
Asked whether the government should bring in an ordinance to restore the provisions of the SC/ST Act which were allegedly diluted by a recent Supreme Court judgement, Kokje said, "The Centre has filed a revision petition in the Supreme Court. After the decision of Supreme Court on this petition, the government has to decide what to do next."
Dalit organisations had called for a Bharat Bandh on April 2 against the Supreme Court's March 20 decision. Several people were killed during the protest.
"People should not agitate against court decisions. The court's decisions should be challenged in the judicial and constitutional way," the new VHP chief said.
Violent clashes between the Dalits and upper castes of the Hindu community couldn't be justified in any way, and the culprits should be punished strictly, he said.
Kokje was elected as VHP's international president last week, defeating senior leader Pravin Togadia's nominee Raghava Reddy, prompting Togadia to quit the organisation.
To a question, Kokje said, "Neither our programs have changed, nor has the way of working. Only office-bearers have changed. The issue of constructing a temple at the Ram Janmabhoomi in Ayodhya is still our priority. We hope the decision of the court in this regard will be out soon."
"Social equality is also included in our main agenda. We do not want any section of the Hindu community to remain backward," he said.
Asked about the VHP's stand on the Common Civil Code, Kokje said, "The subject of Common Civil Code comes under the directive principles of Constitution. These principles were not decided by the RSS. So there should be a Common Civil Code on the basis of these principles; why some people have a problem with this?"