Krolikowski, alongside Willi Stoph and Erich Mielke, was regarded as belonging to the pro-Moscow faction of the Politburo.

In 1988, following the sudden death of Werner Felfe (who had suffered the misfortune to be identified in western media as a possible successor to First Secretary Erich Honecker) Krolikowski regained the Central Committee secretaryship for agriculture.

In November 1989 Werner Krolikowski resigned from his various public offices and on 3 December 1989 he was expelled from what had till very recently been the unchallenged ruling party in East Germany.

An investigation was launched, based on "suspicions of abuse of office and corruption" ("Verdachts auf Amtsmißbrauch u. Korruption").

He gave an interview to the western press in 1992 in which he disclosed that as far back as 1986 Werner Krolikowski had told him, in confidence, that the situation in the SED Politburo had become "unbearable": policy decisions were totally driven by dogma, there was no longer any discussion, there was an absurd level of centralisation and an utterly implausible communications strategy.

[citation needed] After 1966 the "Patriotic Order of Merit", which Krolikowski received " ("for services to the people and the fatherland" ("Für Verdienste um Volk und Vaterland") was awarded at three different levels, designated respectively bronze, silver and gold, so that particularly long standing providers of exceptional service not infrequently won it more than once.