Sania's father Imran termed the reports as "malicious and ridiculous rumours".
"I don't know who is spreading these malicious and ridiculous rumours about Shoaib missing a practice session due to spending time with his wife, Sania. These are baseless and childish allegations," Imran said.
"Shoaib and Sania are both seasoned professional sportsmen who will not allow their personal life to interfere with their professions. Shoaib has a healthy batting average of around 40 on the English tour but will naturally play only when the team management is convinced when his team needs him and when they feel he is back at his best form," Imran said.
Pakistan team manager Yawar Saeed has clarified that Shoaib's exclusion was not in anyway related to indiscipline and the reason for his dropping was poor form.
Pakistan began their two-Test series against Australia on Tuesday at Lord's in London.
Shoaib made a comeback to the Pakistan team after the lifting of a ban and fine on him which was imposed for disciplinary issues.
Photograph: Snaps India