Assistant Chief Constable John Mauger hit out at Sir Stephen House in a memo to force watchdog the Scottish Police Authority (SPA).
He criticised the chief constable for his decision to step up the visibility of armed patrols and also raised questions over the selection process for senior officers.
Referring to armed patrols, he stated in an email: "I want to place on record I am opposed to this escalation and I believe others may be as well. However, there's a climate of fear within Police Scotland in my view."
Mr Mauger claimed that despite being the country's most experienced firearms chief, he was never consulted about the controversial decision which is now the subject of two investigations by police regulators. He also criticised Sir Stephen for using the Dunblane massacre to justify armed patrols at a meeting earlier this year.
The chief constable cited the 1996 school shooting, as well as the 2010 Cumbria shootings by Derrick Bird, to argue his case that officers should not have to spend up to 20 minutes arming themselves in the event of an incident.
Mr Mauger's email, which has been sent to SPA chairman Vic Emery as well as MSPs on Holyrood's justice committee, stated: "For the CC to somehow infer that his policy may have prevented this is simply awful."
The officer - who was cleared of misconduct allegations in May - also went on to raise concerns over the chief constable's selection process for senior roles, claiming it has caused disquiet within the force.
He said: "I am growing increasingly concerned the CC is trying to move Scotland out of the national selection process for chief officers - as the Superintendents Association have said - so the CC can tap who he wants on the shoulder."
However, he added no-one will voice their concerns, stating: "They will not expose themselves as they are afraid."
Mr Mauger was placed on gardening leave in 2010 amid allegations of insubordination and inefficiency after clashing with his Central Scotland Police boss.
He was off work for three years while an investigation was carried out - receiving more than £104,000 a year.
In May this year, the SPA confirmed all complaints and conduct issues against him had been "discharged" after taxpayers footed a bill for £1 million for his paid leave and legal fees.
A Police Scotland spokeswoman has said the force is unaware of Mr Mauger's email.
She added: "Not having seen the latest correspondence from ACC Mauger we are unable to comment at this time."