Reports emerged on Wednesday suggesting Silva's transfer had been held up after the Premier League club missed the deadline to register him by 14 seconds.
A day later the Portuguese outfit released details of the deal, worth up to €29.5 million, and then on Friday Shakespeare spoke out on the issue.
"We know that a deal has been agreed between the clubs, but we're still trying to finalise it," said the Foxes boss ahead of Saturday's home match against champions Chelsea.
"For me, as a football person, of course it's a very rare occasion.
"My thoughts are with the player, but at the moment I'm trying to prepare the team for a really important game on Saturday.
"From my point of view, as a manager, you identify the players and leave the other bits to the legal people."
Leicester confirmed they were still working to ensure Silva's move could be completed and Shakespeare will not allow himself to be distracted by it, despite being eager to have the Portugal international at his disposal.
He added: "It's important at the moment to keep a level head about it and let the legal people get on with it. Purely from a football point of view, we've identified the player and I would love the player to be in with us.
"At this stage, we need to let them carry on with it and hopefully when we're told the players ours, he can train with us and we can welcome him with open arms.
"He's a proven international. On the recruitment side of it, he was identified a long time ago."