He was removed as editor of Deshabhimani when leaders of the provincial Communist Party felt he did not adhere to the party line. He opposed the policy of some state level leaders and other leftist intellectuals to accept foreign funding of political work. He was also for a time the editor of the controversial periodical "Padom", notably criticising a Kerala state government program called People's Campaign for Decentralised Planning (People's Plan) and its creator Thomas Isaac. Vijayan and Professor Sudheesh's articles in "Padom" against the "people's plan", a program aimed at decentralisation of power, became a controversial issue. Later a Kerala court ruled that the allegations of foreign funding of the Kerala Sasthra Sahithya Parishad (KSSP) had been proven by Sudheesh and Vijayan.[https://web.archive.org/web/20071009120933/http://mathrubhumi.com/php/showNews.php?news_category_id=3&Farc=] Vijayan and Sudheesh had started "Paatom" in 2000, and started to attack on CPI(M)'s social democratic stands and attitude towards World Bank and IMF . He resigned from Purogamana Kala Sahithya Sangham as a result of a disagreement with M. A. Baby, then in charge of the CPI(M).