Property consultant Graham Waddell, co-founder of Glasgow-based Johnston Waddell, highlighted the investor caution with just 45 days to go until the historic poll.
Mr Waddell, who set up the firm with David Johnston in 2009, said there was "no doubt" uncertainty caused by the vote has slowed the commercial property sector. His comments chime with speculation in the industry that investors are making provisions to account for the prospect of a Yes vote.
But the claims were countered by pro-independence group Business for Scotland (BfS).
Kenny Anderson, managing director of Anderson Construction and Anderson Buchan Property, and leader of the BfS group in Aberdeen, insisted the debate has not slowed the market, stating he has not heard of any requests for independence clauses.
Mr Waddell, whose firm has advised UK Steel Enterprise and Scottish Council for Development and Industry, said: "There are people who are delaying decisions and there are people who are waiting because of the uncertainty the vote has generated.
"We have a client recently who said, yes they would be interested in buying an investment we had put to them, but only on the basis that they can insert an independence cause which we have learned has been put in various contracts.
"[He said] yes he will buy - subject to a No vote."
While he said the uncertainty over Scotland's constitutional future was holding up investment decisions, Mr Waddell conceded others may see the impasse as an opportunity to press ahead with deals.
"But in my view I don't think there is any doubt it is having a detrimental effect at the moment," he added, "certainly at the level we operate, which is probably sub-£10 million.
"I would say the recovery has stalled a wee bit in Scotland because of the uncertainty."
Mr Waddell added that a Yes vote would be "very bad news for our business" which would bring "further uncertainty" until the process of Scotland becoming an independent nation is concluded.
But equally he anticipates a "bounce" in the property market in the final quarter of the year if the status quo is maintained.
However Mr Anderson said the days after independence would immediately bring "a ton of opportunities for canny business heads".
He stated: "I buy and sell property all the time, I haven't seen any slowdown in the market caused by the referendum debate and I haven't heard of anyone asking for an independence clause to go in the deal.
He added: "Scotland's property market is healthy and moving along, recovering from blows caused by mismanagement of the economy and current UK Governments.
"People are trading in Scottish property and we're seeing increasing value as well as healthy interest in the market."
Mr Waddell was speaking as Johnston Waddell reaps the benefits of a platform likened to "Ebay for property".
The facility, run under franchise from London-based Singer Vielle, allows the firm to present and market properties to potential purchasers online. Believed to be the only system of its kind to be available in Scotland, it gives view aerial shots and street-level footage of properties and their surrounding areas in real time, as well as access to legal documents in an online data room.
Mr Waddell said the site effectively means a property can be purchased almost entirely online.
The only part of the bargain which can't be concluded is the buyer's signature, with electronic signatures not yet legally binding Scotland.
Johnston Waddell is using the service to market properties to its database of 11,000 potential buyers.
While Mr Waddell would not be drawn on actual numbers, he hopes the service will help the firm realise its goal He said: "The attraction to sellers, to our clients who are selling, is that it can be done very, very quickly. In fact, we brought a property to market in Aberdeen and it sold within 10 days to an overseas buyer.
"If we hadn't been part of this company we would never have access to that buyer and have never been able to transact in this way."
Ricky Murray, partner at accountancy firm Johnston Carmichael, said: "Johnston Waddell is a great example of a Scottish SME being innovative by using new technology to enhance their service to clients and, at the same time, give themselves a commercial advantage in a competitive marketplace."