Concerns have emerged at the depth of ousted minister Heather Roy's relationship with her most senior adviser, whose Beehive security clearance had just been blocked after an investigation into his background.

The Security Intelligence Service withheld security clearance for Simon Ewing-Jarvie, a former New Zealand Army lieutenant colonel, shortly before he took part in an Act Party insurrection.

The battle within Act ended in Roy being ousted as deputy leader, dumped as a minister, and sent on two weeks' leave. Ewing-Jarvie also left and was stripped of all access to Parliament and its computer systems.

It is understood that the shutdown process was pre-planned because of the concerns raised by the security review.

Political confidantes of Roy have expressed concern over the advice she has been receiving from Ewing-Jarvie and the depth of their relationship.

The Herald on Sunday observed Roy leaving Ewing-Jarvie's home yesterday morning.

Her car, which was parked outside his house at 10.30pm on Friday, was in the same place at 7am. Neither returned calls.

Ewing-Jarvie had worked for Roy since she was appointed as Minister of Consumer Affairs and, critically, Associate Minister of Defence.

The role gave Roy - and Ewing-Jarvie as her adviser - access to key military secrets and information of critical importance to the security of New Zealand.

Ewing-Jarvie was placed in a key position in Roy's office, where he personally amended drafts of the New Zealand Defence Force review.

Act leader Rodney Hide said the concerns about Ewing-Jarvie had been handled "appropriately by ministerial security".

Early this month, SIS officers working on a standard investigation into the adviser's background decided he should not be allowed to see or access classified material.

In the first week of August, Prime Minister John Key's chief of staff Wayne Eagleson was sent a document stating that Ewing-Jarvie's status had shifted to "non-access to any classified material".

Security checks are usually straightforward, with SIS officers checking disclosures by staff against paper records, tracking an individual's life to the present. Any variation results in closer scrutiny.

SIS officers had been attempting to carry out the clearance work on Ewing-Jarvie for most of the year but had difficulty pinning him down to discuss details.

Documents that emerged following Roy's dumping showed Ewing-Jarvie was heavily involved in a wide-ranging review of New Zealand's defence capabilities and funding.

The details were contained in an 82-page dossier leaked to media and bloggers after Roy's dumping. The document painted Hide as a bully and reflected the dysfunctional relationship he shared with Roy.

Blogger Cameron Slater identified Ewing-Jarvie as both creating and leaking the dossier.

The Prime Minister's spokesman said Key's office had "no concerns" regarding Ewing-Jarvie.