The justification Suharto gave for establishing MUI (Ulama Council of Indonesia) in 1975 was to unite Indonesian ulama (religious scholars). Its role was to issue national fatwas and publicise government policies. However, throughout the New Order, MUI constituted a strong case of co-optation. Suharto pressed MUI to adopt Pancasila and not to issue fatwas that conflicted with state wishes (Hooker, 1997, p. 16). Bramantyo observed MUI's “main function was to coerce the population into accepting government programs that were problematic in respect to Islamic tradition, such as mandatory birth control or raising money through the sale of national lottery tickets” (Bramantyo, 2009). As such, MUI was derided as “Majelis ‘Ular’ Indonesia” (Council of Indonesian Snakes) (Feillard, 2010, p. 172).

However, recent research paints a more subtle picture of the changing behaviour of MUI ulama: from being state stooges to asserting themselves and making progress towards state capture (Moch Nur, 2005, 2010; Nadirsyah, 2004; Ricklefs, 2012; Wahiduddin, 2004). These works suggest that MUI influenced President Susilo Bambang Yudhoyono's government more than it did under previous regimes. Ricklefs (2012) suggest that in the post-Suharto era, government was becoming a tool of MUI (p. 319). A clear example, Ricklefs notes, is Yudhoyono's opening speech of MUI's 7th MUNAS in 2005:

Another stigma associated with MUI today is that the institution is promoting conservatism and aspiring to purify Indonesian Islam (Crouch, 2009, p. 8; Feillard and Madinier, 2011, pp. 256-259; Nasir, 2014; Ricklefs, 2012; Riddell, 2001, pp. 300-302). Scholars and journalists have accused MUI's fatwas of fanning hatred of religious minorities, including Ahmadiyahs, Shias, and liberal Muslim groups. Some conservative and fundamentalist Muslim groups have also used MUI fatwas to voice their unhappiness towards non-Muslim leaders.