The CPEC is a planned network of roads, railways and energy projects linking southern Pakistan, and the Gwadar Port, to China's restive Xinjiang Uyghur autonomous region.
As it passes through the Pakistan-occupied Kashmir (PoK), India has raised objection to the project.
Gen Zubair Mahmood Hayat, the Chairman Joint Chiefs of Staff Committee, alleged that India's Research and Analysis Wing was targeting the CPEC thorough "subversive activities".
The highest-ranking military officer in the Pakistan Defense Forces made the remarks while addressing a passing out parade of the Navy Cadets here.
He also said that peace and stability in Afghanistan was vital for regional security.
Pakistan regularly accuses India of carrying out sabotage activities. India has repeatedly dismissed all such allegations and asserted that cross border terrorism being perpetrated by Pakistan-based groups must stop.