Leading clinician Dr Neil Dewhurst has hit back at Mr Neil's assertions, by quoting Scottish Government statistics, which show the number of hospital beds fell by more than 400 in two years.
It is the latest exchange between the minister and Dr Dewhurst, who steps down as president of the Royal College of Physicians of Edinburgh this week.
On Monday the college issued a statement to mark the end of Dr Dewhurst's term in office in which he said: "Reductions in the numbers of acute beds while medical admissions have continued to rise, in parallel with workforce shortages, have placed almost intolerable pressure on our doctors and nurses."
Mr Neil said: "I would be the last person to deny that there are pressures in the NHS, but it is not all the doom and gloom that is being painted. Indeed some of the facts are contradictory to some of the statements that have been made. For example, Neil Dewhurst said the number of beds have been cut.
"That is not true. Over the last year we have increased the number of beds in the NHS by over 400."
Figures obtained from the statistics division of NHS Scotland showed 16,154 beds in major hospitals last September, down from 16,558 in September 2011.
Dr Dewhurst said: "Earlier this week, the Scottish Government disputed our assertion that the number of beds had been cut in Scottish hospitals. This intervention was both misleading and ill-informed. The latest bed statistics published by Information Services Division on 20 December 2013 show that during the period September 2011 - September 2013 the total number of beds across all medical specialties had been reduced by 404 and in acute medicine, where the pressures are greatest, by 105."
Acute medicine is one of the key medical fields looking after the growing number of elderly patients with complex needs.
The same figures also show average occupancy rates for hospital beds, with the percentage occupied in September at 81.9%. However, Dr Dewhurst questioned whether the way these rates were calculated reflected the reality.
He said: "During times of pressure additional beds have been opened or found and then closed once the pressures have reduced.
"Bed capacity has then been presented as a total of the number of beds being used during these periods.
"Recording the number of beds in this manner has served to present total bed capacity within an acceptable level over the year rather than accurately reflecting periods in which acute medical units and wards were well beyond capacity."
Health Secretary Alex Neil said: "The number of staffed beds varies throughout the year to reflect demand, although the most recent official statistics demonstrate there has been an increase of 140 beds in the year.
"To ensure we have the right number of beds in the right place, we're developing an evidenced-based bed planning tool. This new tool will review capacity on an ongoing basis and will see that our NHS continues to always be able to meet the demands placed upon it."
He added the figures on beds related to staffed beds.