Right of citizenship
This is an uncertain area of Canadian citizenship law. The Citizenship Act requires individuals to be resident in Canada for 1095 days in the four years immediately before they apply for citizenship. Canadian courts have interpreted the word “resident” in different ways. One meaning requires you to be physically present in Canada for all of the 1095 days and one day less would not qualify you for citizenship. The other meaning suggests that as long as you have established your regular residence in Canada then even if you were absent for a few days in between and then returned to Canada, your days of absence would still count as days of “residence”.
In response to your question, if you apply for citizenship with 1000 days of physical presence, your application would most likely be refused by Citizenship and Immigration Canada. You can appeal the refusal. An immigration judge will hear your appeal and it is unclear which of the two above meanings they would apply in your case. Neither is “wrong”. Therefore, it is not a guaranteed situation. Even if you get a positive outcome on appeal, the process takes a very long time, sometimes up to four years after your application.
It is, therefore, advisable that you wait until you have 1095 days of physical presence in Canada before applying for citizenship. You do not need to be in Canada for the 1095 days consecutively. You can leave and return as long as you have a total of 1095 days in the four years immediately before the date of your application.