The National Black Police Association (NBPA) also threatened a recruitment boycott after Assistant Commissioner Tarique Ghaffur was relieved of duties.
Mr Ghaffur has alleged that Sir Ian Blair, head of the Met, racially discriminated against him.
The NBPA wants an urgent meeting with the Home Secretary over the issue.
The association wants Jacqui Smith to appoint an independent figure to mediate between the two sides.
Mr Ghaffur is taking his claim of racial and religious discrimination to a tribunal.
‘Business as usual’
The row between Met bosses and Mr Ghaffur escalated following comments made by the Asian officer at a news conference.
Deputy Commissioner Sir Paul Stephenson said it was inappropriate for the row to be conducted in public and said Mr Ghaffur should “shut up”.
Sir Ian has said the decision to temporarily relieve Mr Ghaffur of his responsibilities was because of the way he had “chosen to conduct himself” in the media.
But the NBPA insisted it was being viewed as an “attack on black officers”.
The source claimed that “veiled threats” of disciplinary action had been made by the Met against the chairman of the Met’s Black Police Association, Alfred John, for statements and comments that he made at the Ghaffur news conference.
The NBPA is arranging an emergency meeting for its officials on Thursday or Friday to consider what action it can take.
Among other ideas being considered by its members will be a vote of no confidence in Sir Ian.
A Scotland Yard spokesman said this morning that it was “business as normal” and dismissed suggestions that a “race war” was engulfing the organisation.
BBC