Pottu Amman returned to Sri Lanka in 1987. He was sent to the Eastern Province where he was the LTTE's associate commander for Batticaloa District. He clashed often with the ambitious Karuna Amman who wanted to eastern regional commander. One of the factors leading to Karuna's defection to the Sri Lankan government in 2004 was his rivalry with Pottu Amman. Pottu Amman was recalled to Jaffna, and in October 1987, when war had erupted between the LTTE and the Indian Peace Keeping Force (IPKF), he was sent to Tamil Nadu to co-ordinate the flow of supplies from India to Sri Lanka. He was briefly jailed in India for smuggling. He returned to Jaffna to take part in military operations against the IPKF and was briefly Jaffna commander. After being injured in the stomach he moved to the Vanni to recover.