Hardjono became an assistant to Abdurrahman Wahid in 1998. After Wahid was elected president, she served as his State Secretary beginning in November 1999. As State Secretary, she worked to promote freedom of the press and is noted as having built the first civilian Presidential office since the fall of Sukarno 35 years prior. Her other duties included the preparation for state functions attended by the president and vice president as well as presidential tours. She also dealt with the press and performed administration duties, which included the supervision of 500 civil servants in charge of the maintenance of the presidential residences. However, according to The Jakarta Post sources at the Merdeka Palace reported that she did not get along well with Wahid's wife Sinta Nuriyah; Furthermore, she was also unpopular with clerics within the Muslim organisation Nahdlatul Ulama, which served as Wahid's political power base, because they disputed her claims that she was descended from an eminent 19th century kyai. Ratih was also accused of being an Australian spy due to her connections to Australia. Greg Sheridan, foreign editor of The Australian, has dismissed the spying accusations as having no shred of evidence, and attributes it to internal government politicking against Kim Beazley.Greg Sheridan, "Artificial Intelligence", The Australian, Edition 1 - All Round Country, Thursday 1 July 2011, p. 016.
