In standard communication information is carried by particles or waves. Counterintuitively, in counterfactual communication particles and information can travel in opposite directions. The quantum Zeno effect allows Bob to transmit a message to Alice by encoding information in particles he never interacts with. The first suggested protocol not only required thousands of ideal optical components, but also resulted in a so-called weak trace of the particles having travelled from Bob to Alice, calling the scalability and counterfactuality of previous proposals and experiments into question. Here we overcome these challenges, implementing a new protocol in a programmable nanophotonic processor, based on reconfigurable silicon-on-insulator waveguides that operate at telecom wavelengths. This, together with our telecom single-photon source and highly-efficient superconducting nanowire single-photon detectors, provides a versatile and stable platform for a high-fidelity implementation of genuinely trace-free counterfactual communication, allowing us to actively tune the number of steps in the Zeno measurement, and achieve a bit error probability below 1%, with neither post-selection nor a weak trace. Our demonstration shows how our programmable nanophotonic processor could be applied to more complex counterfactual tasks and quantum information protocols.