Dom João Garcia Sarmento induced a certain Vithoji to travel to the court of Tirumalai Naikaar in Madurai with Dom Henrique da Cruz and some chiefs of Parava in late 1646. They argued here that the Dutch East India Company had not made its promise to give them annual gifts, and had asked for their expulsion. An bid of 9000 Guilders to Sivanandiappa Pillai and 15000 Guilders to Tirumalai Naikkar was made.The Naikaar, however, was not convinced, and did not allow the Dutch to be expelled. Tirunelveli's governor, Deva Chatira Ayya, was alleged to have taken a bribe of 3000 reals after two years, for looking the other way when the Paravas attacked Kayalpatnam 's Dutch settlement.
In June 1648, the company residents vacated Kayalpatnam along with their movable property, by the yacht Lilli to Galle. Soon after this the company factory was plundered and destroyed.
Joan Maetsuycker, the Dutch governor of Ceylon, led a force of 436 Europeans in an assault on the Portuguese, in 1649. In the course of this conflict, the Dutch occupied the Portuguese possessions at Thiruchendur, Tuticorin and also the Murugan Temple. The temple was fortified, and used as a garrison. The temple's gold and silver was openly ransacked by the troops. Local people made several futile attempts to gain control of the temple, and finally, Thirumalai Nayak made a formal complaint. Nayak mediated between the Dutch and the locals, urging the Dutch to vacate the site, and also to leave along the sea route to avoid further attacks on them.
On 1 March 1649, the Tiruchendur Temple was captured and used a base to launch attacks on Tuticorin's Portuguese interests. Dutch soldier Johann von der Behr of Leipzig (1620-1680) and Johan de Vogel who is a junior merchant and secretary identify the events.
The Dutch are said to have tried to destroy the structure by setting up fire and bombardment while vacating the temple. However their efforts were futile with the mandapams resisting their attack on the battery.
The Dutch decided to carry away the idol of the principal deity of Shanmukhar and Siva Natarajar, as they thought it was made of gold. Initial attempts to melt the metal idols proved futile, and they took the idols by sea. Once at sea, however, a wild storm occurred and the vessel was shaking violently. Frightened that the idols had caused the bad weather, the Dutch sailors threw away the idol at sea. Meanwhile, the locals reported the loss of the idol to Vadamalaiyappa Pillaiyyan, the Madurai Naikaar local governor of Tirunelveli. Thereafter, Pillaiyan ordered the creation of a new idol, and this was made and transported to Tiruchendur.