Plouffe said he would donate his speaking fee to pro-democracy groups, after RFE/RL reported that his trip to Azerbaijan was at the invitation of a pro-government organization.
The Baku-based Institute for Reporters' Freedom and Safety has already prepared a proposal to use the money.
The institute's head, Emin Huseynli, told RFE/RL that he will "send a proposal to Plouffe asking him to allocate $50,000 to the families of journalists in jail. They are in need -- some can't afford medical treatment, some can't even afford transportation to visit their siblings in prison."
Currently, three prominent opposition journalists are jailed in Azerbaijan.
Another civil rights activist, Arzu Abdullayeva, believes Plouffe's money would better serve in supporting human rights NGOs and watchdogs monitoring Azerbaijan's oil and gas sector.
Other NGOs have called for Plouffe to give the money to local election observers, especially pertinent now as Azerbaijan will be holding a referendum on March 18 on whether to scrap the two-term limit, a step that could allow President Ilham Aliyev to remain in power long after his term ends in 2013.
Media experts say there is no legal prohibition on foreigners' funding local NGOs.
Plouffe's decision to give money to local NGOs will disappoint officials in Baku. The Azerbaijani government was hoping that a visit from Plouffe would open up a channel to Barack Obama -- instead it has just resulted in more funding for the democratic opposition.
-- Kenan Aliyev/Arifa Kazimova